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Nabi B, Kumawat M, Yadav PK, Ahlawat N, Mir MA, Kumar V, Kumar M, Ahlawat S. Molecular Prediction and Correlation of the Structure and Function of Universal Stress Protein A (UspA) from Salmonella Typhimurium. Biochem Genet 2024:10.1007/s10528-024-10699-4. [PMID: 38427123 DOI: 10.1007/s10528-024-10699-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 01/13/2024] [Indexed: 03/02/2024]
Abstract
Salmonella Typhimurium (ST) is a zoonotic pathogen that can cause gastroenteritis in humans when they consume contaminated food or water. When exposed to various stressors, both from living organisms (biotic) and the environment (abiotic), Salmonella Typhimurium produces Universal Stress Proteins (USPs). These proteins are gaining recognition for their crucial role in bacterial stress resistance and the ability to enter a prolonged state of growth arrest. Additionally, USPs exhibit diverse structures due to the fusion of the USP domain with different catalytic motifs, enabling them to participate in various reactions and cellular activities during stressful conditions. In this particular study, researchers cloned and analyzed the uspA gene obtained from poultry-derived strains of Salmonella Typhimurium. The gene comprises 435 base pairs, encoding a USP family protein consisting of 144 amino acids. Phylogenetic analysis demonstrated a close relationship between the uspA genes of Salmonella Typhimurium and those found in other bacterial species. We used molecular dynamics simulations and 3D structure prediction to ensure that the USPA protein was stable. Furthermore, we also carried out motif search and network analysis of protein-protein interactions. The findings from this study offer valuable insights for the development of inhibitors targeted against Salmonella Typhimurium.
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Affiliation(s)
- Bilkees Nabi
- Department of Biochemistry & Biochemical Engineering, SHUATS, Prayagraj, 211007, India
| | - Manoj Kumawat
- Department of Microbiology, ICMR- National Institute for Research in Environmental Health, Bhopal, 462030, India
| | - Pramod Kumar Yadav
- Department of Computational Biology & Bioinformatics, SHUATS, Prayagraj, 211007, India
| | - Neeraj Ahlawat
- Department of Animal Husbandry and Dairying, SHUATS, Prayagraj, 211007, India
| | - Manzoor Ahmad Mir
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, 190006, India
| | - Vivek Kumar
- Department of Computational Biology & Bioinformatics, SHUATS, Prayagraj, 211007, India
| | - Manoj Kumar
- Department of Microbiology, ICMR- National Institute for Research in Environmental Health, Bhopal, 462030, India.
| | - Sushma Ahlawat
- Department of Biochemistry & Biochemical Engineering, SHUATS, Prayagraj, 211007, India.
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Zhong S, Yang H, Guan J, Shen J, Ren T, Li Z, Tan F, Li Q, Luo P. Characterization of the MADS-Box Gene Family in Akebia trifoliata and Their Evolutionary Events in Angiosperms. Genes (Basel) 2022; 13:genes13101777. [PMID: 36292662 PMCID: PMC9601569 DOI: 10.3390/genes13101777] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Abstract
As the largest clade of modern plants, flower plants have evolved a wide variety of flowers and fruits. MADS-box genes play key roles in regulating plant morphogenesis, while basal eudicots have an evolutionarily important position of acting as an evolutionary bridge between basal angiosperms and core eudicots. Akebia trifoliata is an important member of the basal eudicot group. To study the early evolution of angiosperms, we identified and characterized the MADS-Box gene family on the whole-genome level of A. trifoliata. There were 47 MADS-box genes (13 type I and 34 type II genes) in the A. trifoliata genome; type I genes had a greater gene length and coefficient of variation and a smaller exon number than type II genes. A total of 27 (57.4%) experienced whole or segmental genome duplication and purifying selection. A transcriptome analysis suggested that three and eight genes were involved in whole fruit and seed development, respectively. The diversification and phylogenetic analysis of 1479 type II MADS-box genes of 22 angiosperm species provided some clues indicating that a γ whole genome triplication event of eudicots possibility experienced a two-step process. These results are valuable for improving A. trifoliata fruit traits and theoretically elucidating evolutionary processes of angiosperms, especially eudicots.
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Affiliation(s)
- Shengfu Zhong
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Huai Yang
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Ju Guan
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Jinliang Shen
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Tianheng Ren
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhi Li
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Feiquan Tan
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Qing Li
- Department of Biology and Chemistry, Chongqing Industry and Trade Polytechnic, Chongqing 408000, China
| | - Peigao Luo
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricutural University of Sichuan Province, College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence:
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3
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Xue Y, Ma L, Wang H, Hao P, Cheng S, Su Z, Li L, Yu S, Wei H. The MADS transcription factor GhFYF is involved in abiotic stress responses in upland cotton (Gossypium hirsutum L.). Gene 2022; 815:146138. [PMID: 34979233 DOI: 10.1016/j.gene.2021.146138] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/06/2021] [Accepted: 12/20/2021] [Indexed: 11/26/2022]
Abstract
Cotton is an important textile industry raw material crops, which plays a critical role in the development of society. MADS transcription factors (TFs) play a key role about the flowering time, flower development, and abiotic stress responses in plants, but little is known about their functions on abiotic stress in cotton. In this study, a MIKCC subfamily gene from cotton, GhFYF (FOREVER YOUNG FLOWER), was isolated and characterized. Our data showed that GhFYF localized to the nucleus. A β-glucuronidase (GUS) activity assay revealed that the promoter of GhFYF was mainly expressed in the flower and seed of ProGhFYF::GUS transgenic A. thaliana plants. The GUS staining of flowers and seeds was deepened after drought, salt treatment, and the expression level of the GUS gene and corresponding stress genes AtERD10, AtAnnexin1 are up-regulated in the inflorescence. Overexpression GhFYF in A. thaliana could promote the seed germination and growth under different salt concentrations, and determin the proline content. Yeast two-hybrid (Y2H) assays showed that GhFYF interacted with the HAD-like protein GhGPP2, which has responds to abiotic stress. Our findings indicate that GhFYF is involved in abiotic stress responses, especially for salt stress. This work establishes a solid foundation for further functional analysis of the GhFYF gene in cotton.
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Affiliation(s)
- Yujun Xue
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Liang Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Pengbo Hao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Shuaishuai Cheng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Zhengzheng Su
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Lin Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
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Chen Y, Shen Q, Lyu P, Lin R, Sun C. Identification and expression profiling of selected MADS-box family genes in Dendrobium officinale. Genetica 2019; 147:303-313. [PMID: 31292836 DOI: 10.1007/s10709-019-00071-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/05/2019] [Indexed: 11/24/2022]
Abstract
Dendrobium officinale, a herb with highly medicinal and ornamental value, is widely distributed in China. MADS-box genes encode transcription factors that regulate various growth and developmental processes in plants, particular in flowering. However, the MADS-box genes in D. officinale are largely unknown. In our study, expression profiling analyses of selected MADS-box genes in D. officinale were performed. In total, 16 DnMADS-box genes with full-length ORF were identified and named according to their phylogenetic relationships with model plants. The transient expression of eight selected MADS-box genes in the epidermal cells of tobacco leaves showed that these DnMADS-box proteins localized to the nucleus. Tissue-specific expression analysis pointed out eight flower-specific expressed MADS-box genes in D. officinale. Furthermore, expression patterns of DnMADS-box genes were investigated during the floral transition process. DnMADS3, DnMADS8 and DnMADS22 were significantly up-regulated in the reproductive phase compared with the vegetative phase, suggesting putative roles of these DnMADS-box genes in flowering. Our data showed that the expressions of MADS-box genes in D. officinale were controlled by diverse exogenous phytohormones. Together, these findings will facilitate further studies of MADS-box genes in Orchids and broaden our understanding of the genetics of flowering.
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Affiliation(s)
- Yue Chen
- Institute of Horticulture, Zhejiang Academy of Agriculture Science, Hangzhou, Zhejiang, People's Republic of China.,Key laboratory of creative Agriculture, Ministry of Agriculture, Hangzhou, People's Republic of China
| | - Qi Shen
- Plant Protection and Microbiology, Zhejiang Academy of Agricultural Science, Hangzhou, Zhejiang, People's Republic of China
| | - Ping Lyu
- Lin'an Agricultural & Forestry Technology Extension Center, Hangzhou, Zhejiang, People's Republic of China
| | - Renan Lin
- Yueqing Forestry Varieties Tech Center, Yueqing, Zhejiang, People's Republic of China
| | - Chongbo Sun
- Institute of Horticulture, Zhejiang Academy of Agriculture Science, Hangzhou, Zhejiang, People's Republic of China. .,Key laboratory of creative Agriculture, Ministry of Agriculture, Hangzhou, People's Republic of China.
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5
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Sen S, Rai R, Chatterjee A, Rai S, Yadav S, Agrawal C, Rai LC. Molecular characterization of two novel proteins All1122 and Alr0750 of Anabaena PCC 7120 conferring tolerance to multiple abiotic stresses in Escherichia coli. Gene 2019; 685:230-241. [PMID: 30448320 DOI: 10.1016/j.gene.2018.11.038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 09/28/2018] [Accepted: 11/08/2018] [Indexed: 11/19/2022]
Abstract
In- silico and functional genomics approaches have been used to determine cellular functions of two hypothetical proteins All1122 and Alr0750 of Anabaena sp. PCC 7120. Motif analysis and multiple sequence alignment predicted them as typical α/β ATP binding universal stress family protein-A (UspA) with G-(2×)-G-(9×)-G(S/T) as conserved motif. qRT-PCR data under UV-B, NaCl, heat, As, CdCl2, mannitol and methyl viologen registered approximately 1.4 to 4.3 fold induction of all1122 and alr0750 thus confirming their multiple abiotic stress tolerance potential. The recombinant E. coli (BL21) cells harboring All1122 and Alr0750 showed 12-41% and 23-41% better growth respectively over wild type control under said abiotic stresses thus revalidating their stress coping ability. Functional complementation on heterologous expression in UspA mutant E. coli strain LN29MG1655 (ΔuspA::Kan) attested their UspA family membership. This study tempted us to suggest that recombinant Anabaena PCC 7120 over expressing all1122 and alr0750 might contribute to the nitrogen economy in paddy fields experiencing array of abiotic stresses including drought and nutrient limitation.
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Affiliation(s)
- Sonia Sen
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Ruchi Rai
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Antra Chatterjee
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Shweta Rai
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Shivam Yadav
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Chhavi Agrawal
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - L C Rai
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
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6
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Nardeli SM, Artico S, Aoyagi GM, de Moura SM, da Franca Silva T, Grossi-de-Sa MF, Romanel E, Alves-Ferreira M. Genome-wide analysis of the MADS-box gene family in polyploid cotton (Gossypium hirsutum) and in its diploid parental species (Gossypium arboreum and Gossypium raimondii). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 127:169-184. [PMID: 29604523 DOI: 10.1016/j.plaphy.2018.03.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 02/27/2018] [Accepted: 03/18/2018] [Indexed: 06/08/2023]
Abstract
The MADS-box gene family encodes transcription factors that share a highly conserved domain known to bind to DNA. Members of this family control various processes of development in plants, from root formation to fruit ripening. In this work, a survey of diploid (Gossypium raimondii and Gossypium arboreum) and tetraploid (Gossypium hirsutum) cotton genomes found a total of 147, 133 and 207 MADS-box genes, respectively, distributed in the MIKC, Mα, Mβ, Mγ, and Mδ subclades. A comparative phylogenetic analysis among cotton species, Arabidopsis, poplar and grapevine MADS-box homologous genes allowed us to evaluate the evolution of each MADS-box lineage in cotton plants and identify sequences within well-established subfamilies. Chromosomal localization and phylogenetic analysis revealed that G. raimondii and G. arboreum showed a conserved evolution of the MIKC subclade and a distinct pattern of duplication events in the Mα, Mγ and Mδ subclades. Additionally, G. hirsutum showed a combination of its parental subgenomes followed by a distinct evolutionary history including gene gain and loss in each subclade. qPCR analysis revealed the expression patterns of putative homologs in the AP1, AP3, AGL6, SEP4, AGL15, AG, AGL17, TM8, SVP, SOC and TT16 subfamilies of G. hirsutum. The identification of putative cotton orthologs is discussed in the light of evolution and gene expression data from other plants. This analysis of the MADS-box genes in Gossypium species opens an avenue to understanding the origin and evolution of each gene subfamily within diploid and polyploid species and paves the way for functional studies in cotton species.
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Affiliation(s)
- Sarah Muniz Nardeli
- Laboratório de Genética Molecular Vegetal, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), CEP 21941-617, Rio de Janeiro, RJ, Brazil.
| | - Sinara Artico
- Laboratório de Genética Molecular Vegetal, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), CEP 21941-617, Rio de Janeiro, RJ, Brazil.
| | - Gustavo Mitsunori Aoyagi
- Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo (EEL-USP), CEP 12602-810, Lorena, SP, Brazil.
| | - Stéfanie Menezes de Moura
- Laboratório de Genética Molecular Vegetal, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), CEP 21941-617, Rio de Janeiro, RJ, Brazil.
| | - Tatiane da Franca Silva
- Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo (EEL-USP), CEP 12602-810, Lorena, SP, Brazil.
| | | | - Elisson Romanel
- Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo (EEL-USP), CEP 12602-810, Lorena, SP, Brazil.
| | - Marcio Alves-Ferreira
- Laboratório de Genética Molecular Vegetal, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), CEP 21941-617, Rio de Janeiro, RJ, Brazil.
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Liu XR, Pan T, Liang WQ, Gao L, Wang XJ, Li HQ, Liang S. Overexpression of an Orchid (Dendrobium nobile) SOC1/TM3-Like Ortholog, DnAGL19, in Arabidopsis Regulates HOS1-FT Expression. FRONTIERS IN PLANT SCIENCE 2016; 7:99. [PMID: 26904066 PMCID: PMC4746357 DOI: 10.3389/fpls.2016.00099] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 01/19/2016] [Indexed: 05/18/2023]
Abstract
Flowering in the appropriate season is critical for successful reproduction in angiosperms. The orchid species, Dendrobium nobile, requires vernalization to achieve flowering in the spring, but the underlying regulatory network has not been identified to date. The MADS-box transcription factor DnAGL19 was previously identified in a study of low-temperature treated D. nobile buds and was suggested to regulate vernalization-induced flowering. In this study, phylogenetic analysis of DnAGL9 and the MADS-box containing proteins showed that DnAGL19 is phylogenetically closely related to the SOC1-like protein from orchid Dendrobium Chao Parya Smile, DOSOC1. The orchid clade closed to but is not included into the SOC1-1/TM3 clades associated with either eudicots or monocots, suggesting that DnAGL19 is an SOC1-1/TM3-like ortholog. DnAGL19 was found to be highly expressed in pseudobulbs, leaves, roots, and axillary buds but rarely in flowers, and to be substantially upregulated in axillary buds by prolonged low-temperature treatments. Overexpression of DnAGL19 in Arabidopsis thaliana resulted in a small but significantly reduced time to bolting, suggesting that flowering time was slightly accelerated under normal growth conditions. Consistent with this, the A. thaliana APETELA1 (AP1) gene was expressed at an earlier stage in transgenic lines than in wild type plants, while the FLOWERING LOCUS T (FT) gene was suppressed, suggesting that altered regulations on these transcription factors caused the weak promotion of flowering. HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE 1 (HOS1) was slightly activated under the same conditions, suggesting that the HOS1-FT module may be involved in the DnAGL19-related network. Under vernalization conditions, FT expression was significantly upregulated, whereas HOS1 expression in the transgenic A. thaliana has a level similar to that in wild type. Taken together, these results suggest that DnAGL19 controls the action of the HOS1-FT module depending on temperature cues, which could contribute to regulation of D. nobile flowering time. These data provide insights into how flowering is fine-tuned in D. nobile to acclimate the plant to seasonal changes in temperature.
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Aguilar-Martínez JA, Uchida N, Townsley B, West DA, Yanez A, Lynn N, Kimura S, Sinha N. Transcriptional, posttranscriptional, and posttranslational regulation of SHOOT MERISTEMLESS gene expression in Arabidopsis determines gene function in the shoot apex. PLANT PHYSIOLOGY 2015; 167:424-42. [PMID: 25524441 PMCID: PMC4326739 DOI: 10.1104/pp.114.248625] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 12/12/2014] [Indexed: 05/21/2023]
Abstract
The activity of SHOOT MERISTEMLESS (STM) is required for the functioning of the shoot apical meristem (SAM). STM is expressed in the SAM but is down-regulated at the site of leaf initiation. STM is also required for the formation of compound leaves. However, how the activity of STM is regulated at the transcriptional, posttranscriptional, and posttranslational levels is poorly understood. We previously found two conserved noncoding sequences in the promoters of STM-like genes across angiosperms, the K-box and the RB-box. Here, we characterize the function of the RB-box in Arabidopsis (Arabidopsis thaliana). The RB-box, along with the K-box, regulates the expression of STM in leaf sinuses, which are areas on the leaf blade with meristematic potential. The RB-box also contributes to restrict STM expression to the SAM. We identified FAR1-RELATED SEQUENCES-RELATED FACTOR1 (FRF1) as a binding factor to the RB-box region. FRF1 is an uncharacterized member of a subfamily of four truncated proteins related to the FAR1-RELATED SEQUENCES factors. Internal deletion analysis of the STM promoter identified a region required to repress the expression of STM in hypocotyls. Expression of STM in leaf primordia under the control of the JAGGED promoter produced plants with partially undifferentiated leaves. We further found that the ELK domain has a role in the posttranslational regulation of STM by affecting the nuclear localization of STM.
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Affiliation(s)
- José Antonio Aguilar-Martínez
- Department of Plant Biology, University of California, Davis, California 95616 (J.A.A.-M., N.U., B.T., D.A.W., A.Y., N.L., S.K., N.S.);World Premier International Research Center Initiative-Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan (N.U.); andDepartment of Bioresource and Environmental Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan (S.K.)
| | - Naoyuki Uchida
- Department of Plant Biology, University of California, Davis, California 95616 (J.A.A.-M., N.U., B.T., D.A.W., A.Y., N.L., S.K., N.S.);World Premier International Research Center Initiative-Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan (N.U.); andDepartment of Bioresource and Environmental Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan (S.K.)
| | - Brad Townsley
- Department of Plant Biology, University of California, Davis, California 95616 (J.A.A.-M., N.U., B.T., D.A.W., A.Y., N.L., S.K., N.S.);World Premier International Research Center Initiative-Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan (N.U.); andDepartment of Bioresource and Environmental Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan (S.K.)
| | - Donnelly Ann West
- Department of Plant Biology, University of California, Davis, California 95616 (J.A.A.-M., N.U., B.T., D.A.W., A.Y., N.L., S.K., N.S.);World Premier International Research Center Initiative-Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan (N.U.); andDepartment of Bioresource and Environmental Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan (S.K.)
| | - Andrea Yanez
- Department of Plant Biology, University of California, Davis, California 95616 (J.A.A.-M., N.U., B.T., D.A.W., A.Y., N.L., S.K., N.S.);World Premier International Research Center Initiative-Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan (N.U.); andDepartment of Bioresource and Environmental Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan (S.K.)
| | - Nafeesa Lynn
- Department of Plant Biology, University of California, Davis, California 95616 (J.A.A.-M., N.U., B.T., D.A.W., A.Y., N.L., S.K., N.S.);World Premier International Research Center Initiative-Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan (N.U.); andDepartment of Bioresource and Environmental Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan (S.K.)
| | - Seisuke Kimura
- Department of Plant Biology, University of California, Davis, California 95616 (J.A.A.-M., N.U., B.T., D.A.W., A.Y., N.L., S.K., N.S.);World Premier International Research Center Initiative-Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan (N.U.); andDepartment of Bioresource and Environmental Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan (S.K.)
| | - Neelima Sinha
- Department of Plant Biology, University of California, Davis, California 95616 (J.A.A.-M., N.U., B.T., D.A.W., A.Y., N.L., S.K., N.S.);World Premier International Research Center Initiative-Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan (N.U.); andDepartment of Bioresource and Environmental Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan (S.K.)
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Zhou T, Fan M, Irfan M, Wang H, Wang D, Wang L, Zhang C, Feng L. Phylogenetic analysis of STK gene family and Usp domain in maize. Mol Biol Rep 2014; 41:8273-84. [PMID: 25326719 DOI: 10.1007/s11033-014-3728-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Accepted: 09/03/2014] [Indexed: 11/28/2022]
Abstract
Serine and threonine kinase STK1 and STK2 play an important regulatory role in the process of pollen development in maize. Six homologous sequences which were similar with STK1 and STK2 having more than 80 % similarity were found at NCBI, and they all belong to STK gene family. Phylogenetic analysis showed that STK family in maize might belong to RLK family. In STK family, gene duplication event was occurred during evolutionary process, and experienced purifying selection after gene duplication and the time of gene duplication was about 12 million years ago. The domains of STK family belongs to single transmembrane protein, which have intracellular conserved kinase catalytic domain and extracellular receptor domain on N-terminal. The evolution of intracellular selection was faster than extracellular selection, and positive selection or weak purifying selection play an important role. Analyzing its unique Usp domain we found that it was located between sensor domain at N-terminal and catalytic domain at C-terminal, which belongs to hydrophobic protein with several phosphorylation sites, acting on serine and threonine protein phosphorylation. The kinship of Usp domain in STK family was close to 35-like protein containing U-box domain, predicting that they might belong to the same family with a similar structure and function, so that we can predict the function of Usp domain in STK family.
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Affiliation(s)
- Ting Zhou
- Biotechnology and Bioscience College, Shenyang Agricultural University, Shenyang, 110866, China
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Duncan EJ, Benton MA, Dearden PK. Canonical terminal patterning is an evolutionary novelty. Dev Biol 2013; 377:245-61. [PMID: 23438815 DOI: 10.1016/j.ydbio.2013.02.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 02/08/2013] [Accepted: 02/14/2013] [Indexed: 10/27/2022]
Abstract
Patterning of the terminal regions of the Drosophila embryo is achieved by an exquisitely regulated signal that passes between the follicle cells of the ovary, and the developing embryo. This pathway, however, is missing or modified in other insects. Here we trace the evolution of this pathway by examining the origins and expression of its components. The three core components of this pathway: trunk, torso and torso-like have different evolutionary histories and have been assembled step-wise to form the canonical terminal patterning pathway of Drosophila and Tribolium. Trunk, torso and a gene unrelated to terminal patterning, prothoraciotrophic hormone (PTTH), show an intimately linked evolutionary history, with every holometabolous insect, except the honeybee, possessing both PTTH and torso genes. Trunk is more restricted in its phylogenetic distribution, present only in the Diptera and Tribolium and, surprisingly, in the chelicerate Ixodes scapularis, raising the possibility that trunk and torso evolved earlier than previously thought. In Drosophila torso-like restricts the activation of the terminal patterning pathway to the poles of the embryo. Torso-like evolved in the pan-crustacean lineage, but based on expression of components of the canonical terminal patterning system in the hemimetabolous insect Acyrthosiphon pisum and the holometabolous insect Apis mellifera, we find that the canonical terminal-patterning system is not active in these insects. We therefore propose that the ancestral function of torso-like is unrelated to terminal patterning and that torso-like has become co-opted into terminal patterning in the lineage leading to Coleoptera and Diptera. We also show that this co-option has not resulted in changes to the molecular function of this protein. Torso-like from the pea aphid, honeybee and Drosophila, despite being expressed in different patterns, are functionally equivalent. We propose that co-option of torso-like into restricting the activity of trunk and torso facilitated the final step in the evolution of this pathway; the capture of transcriptional control of target genes such as tailless and huckebein by this complex and novel patterning pathway.
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Affiliation(s)
- Elizabeth J Duncan
- Laboratory for Evolution and Development, Genetics Otago, Gravida, National Centre for Growth and Development, Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, Aotearoa, New Zealand.
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11
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alr0882 encoding a hypothetical protein of Anabaena PCC7120 protects Escherichia coli from nutrient starvation and abiotic stresses. Gene 2012; 511:248-55. [PMID: 23006586 DOI: 10.1016/j.gene.2012.09.033] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Revised: 05/15/2012] [Accepted: 09/05/2012] [Indexed: 11/20/2022]
Abstract
This study is the first to demonstrate cloning of alr0882, a hypothetical protein gene of Anabaena PCC7120, its heterologous expression in Escherichia coli strain LN29MG1655 (∆uspA::Kan) and functional complementation of abiotic stress tolerance of E. coli UspA. The recombinant vector pGEX-5X-2-alr0882 was used to transform ∆uspA E. coli strain. The IPTG induced expression of a 56.6kDa GST fusion protein was visualized on SDS-PAGE and attested by immunoblotting. E. coli ∆uspA strain harboring pGEX-5X-2-alr0882 when grown under carbon, nitrogen, phosphorus and sulphur limitation and abiotic stresses e.g. nalidixic acid, cycloserine, CdCl(2), H(2)O(2), UV-B, phenazine methosulphate (PMS), dinitrophenol (DNP), NaCl, heat, carbofuron and CuCl(2) demonstrated about 22.6-51.6% increase in growth over the cells transformed with empty vector. Expression of alr0882 gene in mutant E. coli as measured by semi-quantitative RT-PCR at different time points under selected treatments reaffirmed its role in tolerance against stresses employed in this study. Thus the results of this study vividly demonstrated that the novel protein alr0882, although appreciably different from the known UspA of E. coli, offers tolerance to abiotic stresses hence holds potential for the development of transgenic cyanobacteria.
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12
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Schweikhard ES, Kuhlmann SI, Kunte HJ, Grammann K, Ziegler CM. Structure and function of the universal stress protein TeaD and its role in regulating the ectoine transporter TeaABC of Halomonas elongata DSM 2581(T). Biochemistry 2010; 49:2194-204. [PMID: 20113006 DOI: 10.1021/bi9017522] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The halophilic bacterium Halomonas elongata takes up the compatible solute ectoine via the osmoregulated TRAP transporter TeaABC. A fourth orf (teaD) is located adjacent to the teaABC locus that encodes a putative universal stress protein (USP). By RT-PCR experiments we proved a cotranscription of teaD along with teaABC. Deletion of teaD resulted in an enhanced uptake for ectoine by the transporter TeaABC and hence a negative activity regulation of TeaABC by TeaD. A transcriptional regulation via DNA binding could be excluded. ATP binding to native TeaD was shown by HPLC, and the crystal structure of TeaD was solved in complex with ATP to a resolution of 1.9 A by molecular replacement. TeaD forms a dimer-dimer complex with one ATP molecule bound to each monomer, which has a Rossmann-like alpha/beta overall fold. Our results reveal an ATP-dependent oligomerization of TeaD, which might have a functional role in the regulatory mechanism of TeaD. USP-encoding orfs, which are located adjacent to genes encoding for TeaABC homologues, could be identified in several other organisms, and their physiological role in balancing the internal cellular ectoine pool is discussed.
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Affiliation(s)
- Eva S Schweikhard
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
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13
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Degnan PH, Lazarus AB, Wernegreen JJ. Genome sequence of Blochmannia pennsylvanicus indicates parallel evolutionary trends among bacterial mutualists of insects. Genome Res 2005; 15:1023-33. [PMID: 16077009 PMCID: PMC1182215 DOI: 10.1101/gr.3771305] [Citation(s) in RCA: 155] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The distinct lifestyle of obligately intracellular bacteria can alter fundamental forces that drive and constrain genome change. In this study, sequencing the 792-kb genome of Blochmannia pennsylvanicus, an obligate endosymbiont of Camponotus pennsylvanicus, enabled us to trace evolutionary changes that occurred in the context of a bacterial-ant association. Comparison to the genome of Blochmannia floridanus reveals differential loss of genes involved in cofactor biosynthesis, the composition and structure of the cell wall and membrane, gene regulation, and DNA replication. However, the two Blochmannia species show complete conservation in the order and strand orientation of shared genes. This finding of extreme stasis in genome architecture, also reported previously for the aphid endosymbiont Buchnera, suggests that genome stability characterizes long-term bacterial mutualists of insects and constrains their evolutionary potential. Genome-wide analyses of protein divergences reveal 10- to 50-fold faster amino acid substitution rates in Blochmannia compared to related bacteria. Despite these varying features of genome evolution, a striking correlation in the relative divergences of proteins indicates parallel functional constraints on gene functions across ecologically distinct bacterial groups. Furthermore, the increased rates of amino acid substitution and gene loss in Blochmannia have occurred in a lineage-specific fashion, which may reflect life history differences of their ant hosts.
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Affiliation(s)
- Patrick H Degnan
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA
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14
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Feng J, Yuan F, Gao Y, Liang C, Xu J, Zhang C, He L. A novel antimicrobial protein isolated from potato (Solanum tuberosum) shares homology with an acid phosphatase. Biochem J 2003; 376:481-7. [PMID: 12927022 PMCID: PMC1223772 DOI: 10.1042/bj20030806] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2003] [Revised: 08/15/2003] [Accepted: 08/20/2003] [Indexed: 11/17/2022]
Abstract
The nucleotide and amino acids sequences for AP(1) will appear in the GenBank(R) and NCBI databases under accession number AY297449. A novel antimicrobial protein (AP(1)) was purified from leaves of the potato ( Solanum tuberosum, variety MS-42.3) with a procedure involving ammonium sulphate fractionation, molecular sieve chromatography with Sephacryl S-200 and hydrophobic chromatography with Butyl-Sepharose using a FPLC system. The inhibition spectrum investigation showed that AP(1) had good inhibition activity against five different strains of Ralstonia solanacearum from potato or other crops, and two fungal pathogens, Rhizoctonia solani and Alternaria solani from potato. The full-length cDNA encoding AP(1) has been successfully cloned by screening a cDNA expression library of potato with an anti-AP(1) antibody and RACE (rapid amplification of cDNA ends) PCR. Determination of the nucleotide sequences revealed the presence of an open reading frame encoding 343 amino acids. At the C-terminus of AP(1) there is an ATP-binding domain, and the N-terminus exhibits 58% identity with an/the acid phosphatase from Mesorhizobium loti. SDS/PAGE and Western blotting analysis suggested that the AP(1) gene can be successfully expressed in Escherichia coli and recognized by an antibody against AP(1). Also the expressed protein showed an inhibition activity the same as original AP(1) protein isolated from potato. We suggest that AP(1) most likely belongs to a new group of proteins with antimicrobial characteristics in vitro and functions in relation to phosphorylation and energy metabolism of plants.
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Affiliation(s)
- Jie Feng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Beijing, 100094, People's Republic of China
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15
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Abstract
Mycobacterium tuberculosis expresses universal stress proteins (USPs) when its growth is retarded by oxygen depletion. This class of proteins is emerging as being important in the resistance of bacteria to stress and prolonged growth arrest. Here we assess the properties of USPs and their relevance to mycobacteria.
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Affiliation(s)
- Ronan O'Toole
- Department of Biological Sciences, Imperial College London, London, SW7 2AZ, UK.
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16
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Gustavsson N, Diez A, Nyström T. The universal stress protein paralogues of Escherichia coli are co-ordinately regulated and co-operate in the defence against DNA damage. Mol Microbiol 2002; 43:107-17. [PMID: 11849540 DOI: 10.1046/j.1365-2958.2002.02720.x] [Citation(s) in RCA: 119] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We have cloned, characterized and inactivated genes encoding putative UspA paralogues in Escherichia coli. The yecG (uspC), yiiT (uspD) and ydaA (uspE) genes were demonstrated to encode protein pro-ducts and these were mapped to spots in the E. coli proteomic database. Expression analysis using chromosomal transcriptional lacZ fusions and two-dimensional gels revealed that all usp genes analysed are regulated in a similar fashion. Thus, uspC, D and E are all induced in stationary phase and by a variety of stresses causing growth arrest of cells. Induction is independent of rpoS but is abolished in a deltarelA deltaspoT (ppGpp0) background and rescued by suppressor mutations rendering the beta-subunit of RNA polymerase to behave like a stringent polymerase. Ectopic elevation of ppGpp levels in growing cells, by overproducing the RelA protein, triggered the induction of all usp genes. The expression of all usp genes was also elevated by a mutation in the ftsK cell division gene, and this super-induction could be suppressed by inactivating recA indicating that the usp paralogues are involved in the management of DNA. Indeed, uspC, uspD and uspE deletion mutants were all found to be sensitive to UV exposure. Overexpression of UspD could compensate for the lack of a chromosomal uspD gene but not a uspA gene. Similarly, UspA overproduction could only compensate for the lack of chromosomal uspA. Moreover, combination of usp mutations had no additive effect on UV sensitivity indicating that they are all co-operating and required in the same pathway, which could explain the co-ordinated regulation of the genes.
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Affiliation(s)
- N Gustavsson
- Department of Cell and Molecular Biology, Göteborg University, Box 462, SE-405 30 Göteborg, Sweden
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17
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Abstract
BACKGROUND The universal stress protein UspA is a small cytoplasmic bacterial protein whose expression is enhanced several-fold when cellular viability is challenged with heat shock, nutrient starvation, stress agents which arrest cell growth, or DNA-damaging agents. UspA enhances the rate of cell survival during prolonged exposure to such conditions, suggesting that it asserts a general "stress endurance" activity. However, neither the structure of UspA nor the biochemical mechanism by which it protects cells from the broad spectrum of stress agents is known. RESULTS The crystal structure of Haemophilus influenzae UspA reveals an asymmetric dimer with a tertiary alpha/beta fold similar to that of the Methanococcus jannaschi MJ0577 protein, a protein whose crystal structure revealed a novel ATP binding motif. UspA differs significantly from the MJ0577 structure in several details, including the triphosphate binding loop of the ATP binding motif; UspA shows no ATP binding activity. CONCLUSIONS Within the universal stress protein family that is delineated by sequence similarity, UspA is the only member which has been correlated with a cellular activity, and MJ0577 is the only member which has been assigned a biochemical activity, i.e., ATP binding. UspA has a similar fold to the MJ0577 protein but does not bind ATP. This suggests that members of this protein family will segregate into two groups, based on whether or not they bind ATP. By implication, one subset of the universal stress proteins presumably has an ATP-dependent function, while another subset functions in ATP-independent activities.
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Affiliation(s)
- M C Sousa
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
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18
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Nagasaki H, Sakamoto T, Sato Y, Matsuoka M. Functional analysis of the conserved domains of a rice KNOX homeodomain protein, OSH15. THE PLANT CELL 2001; 13:2085-98. [PMID: 11549765 PMCID: PMC139453 DOI: 10.1105/tpc.010113] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2001] [Accepted: 06/21/2001] [Indexed: 05/19/2023]
Abstract
The rice KNOX protein OSH15 consists of four conserved domains: the MEINOX domain, which can be divided into two subdomains (KNOX1 and KNOX2); the GSE domain; the ELK domain; and the homeodomain (HD). To investigate the function of each domain, we generated 10 truncated proteins with deletions in the conserved domains and four proteins with mutations in the conserved amino acids in the HD. Transgenic analysis suggested that KNOX2 and HD are essential for inducing the abnormal phenotype and that the KNOX1 and ELK domains affect phenotype severity. We also found that both KNOX2 and HD are necessary for homodimerization and that only HD is needed for binding of OSH15 to its target sequence. Transactivation studies suggested that both the KNOX1 and ELK domains play a role in suppressing target gene expression. On the basis of these findings, we propose that overproduced OSH15 probably acts as a dimer and may ectopically suppress the expression of target genes that induce abnormal morphology in transgenic plants.
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Affiliation(s)
- H Nagasaki
- BioScience Center, Nagoya University, Chikusa, Nagoya 464-0814, Japan
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19
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Nagasaki H, Sakamoto T, Sato Y, Matsuoka M. Functional analysis of the conserved domains of a rice KNOX homeodomain protein, OSH15. THE PLANT CELL 2001; 13:2085-2098. [PMID: 11549765 DOI: 10.1105/tpc.13.9.2085] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The rice KNOX protein OSH15 consists of four conserved domains: the MEINOX domain, which can be divided into two subdomains (KNOX1 and KNOX2); the GSE domain; the ELK domain; and the homeodomain (HD). To investigate the function of each domain, we generated 10 truncated proteins with deletions in the conserved domains and four proteins with mutations in the conserved amino acids in the HD. Transgenic analysis suggested that KNOX2 and HD are essential for inducing the abnormal phenotype and that the KNOX1 and ELK domains affect phenotype severity. We also found that both KNOX2 and HD are necessary for homodimerization and that only HD is needed for binding of OSH15 to its target sequence. Transactivation studies suggested that both the KNOX1 and ELK domains play a role in suppressing target gene expression. On the basis of these findings, we propose that overproduced OSH15 probably acts as a dimer and may ectopically suppress the expression of target genes that induce abnormal morphology in transgenic plants.
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Affiliation(s)
- H Nagasaki
- BioScience Center, Nagoya University, Chikusa, Nagoya 464-0814, Japan
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20
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Florczyk MA, McCue LA, Stack RF, Hauer CR, McDonough KA. Identification and characterization of mycobacterial proteins differentially expressed under standing and shaking culture conditions, including Rv2623 from a novel class of putative ATP-binding proteins. Infect Immun 2001; 69:5777-85. [PMID: 11500455 PMCID: PMC98695 DOI: 10.1128/iai.69.9.5777-5785.2001] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The environmental signals that affect gene regulation in Mycobacterium tuberculosis remain largely unknown despite their importance to tuberculosis pathogenesis. Other work has shown that several promoters, including acr (also known as hspX) (alpha-crystallin homolog), are upregulated in shallow standing cultures compared with constantly shaking cultures. Each of these promoters is also induced to a similar extent within macrophages. The present study used two-dimensional gel electrophoresis and mass spectrometry to further characterize differences in mycobacterial protein expression during growth under standing and shaking culture conditions. Metabolic labeling of M. bovis BCG showed that at least 45 proteins were differentially expressed under standing and shaking culture conditions. Rv2623, CysA2-CysA3, Gap, and Acr were identified from each of four spots or gel bands that were specifically increased in bacteria from standing cultures. An additional standing-induced spot contained two comigrating proteins, GlcB and KatG. The greatest induction was observed with Rv2623, a 32-kDa protein of unknown function that was strongly expressed under standing conditions and absent in shaking cultures. Analysis using PROBE, a multiple sequence alignment and database mining tool, classified M. tuberculosis Rv2623 as a member of a novel class of ATP-binding proteins that may be involved in M. tuberculosis's response to environmental signals. These studies demonstrate the power of combined proteomic and computational approaches and demonstrate that subtle differences in bacterial culture conditions may have important implications for the study of gene expression in mycobacteria.
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Affiliation(s)
- M A Florczyk
- Department of Biomedical Sciences, University at Albany, Albany, New York 12222, USA
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21
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Diez A, Gustavsson N, Nyström T. The universal stress protein A of Escherichia coli is required for resistance to DNA damaging agents and is regulated by a RecA/FtsK-dependent regulatory pathway. Mol Microbiol 2000; 36:1494-503. [PMID: 10931298 DOI: 10.1046/j.1365-2958.2000.01979.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The link between cell division defects and the induction of the universal stress response is demonstrated to operate via the RecA regulator of the SOS response. An insertion in the cell division gene ftsK upregulates uspA in a recA-dependent manner. Unlike true SOS response genes, this upregulation only occurs in growth-arrested cells and is LexA independent. Thus, besides ppGpp-dependent starvation signals, DNA aberrations transduce RecA-dependent signals to the uspA promoter, which only affect the promoter during stasis. Further, we show that ftsK itself, like uspA, is induced in stationary phase and that this induction requires the stringent control modulon rather than activated RecA. Thus, ftsK, like uspA, is regulated by at least two global regulators: ppGpp of the stringent control network and RecA of the SOS modulon. We suggest that UspA is a new bona fide member of the RecA-dependent DNA protection and repair system, as mutants lacking functional UspA were found to be sensitive to UV irradiation and mitomycin C exposure. Moreover, the UV sensitivity of uspA mutants is enhanced in an additive manner by the ftsK1 mutation.
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Affiliation(s)
- A Diez
- Department of Cell and Molecular Biology--Microbiology, Göteborg University, Sweden
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22
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Alvarez-Buylla ER, Pelaz S, Liljegren SJ, Gold SE, Burgeff C, Ditta GS, Ribas de Pouplana L, Martínez-Castilla L, Yanofsky MF. An ancestral MADS-box gene duplication occurred before the divergence of plants and animals. Proc Natl Acad Sci U S A 2000; 97:5328-33. [PMID: 10805792 PMCID: PMC25828 DOI: 10.1073/pnas.97.10.5328] [Citation(s) in RCA: 321] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Changes in genes encoding transcriptional regulators can alter development and are important components of the molecular mechanisms of morphological evolution. MADS-box genes encode transcriptional regulators of diverse and important biological functions. In plants, MADS-box genes regulate flower, fruit, leaf, and root development. Recent sequencing efforts in Arabidopsis have allowed a nearly complete sampling of the MADS-box gene family from a single plant, something that was lacking in previous phylogenetic studies. To test the long-suspected parallel between the evolution of the MADS-box gene family and the evolution of plant form, a polarized gene phylogeny is necessary. Here we suggest that a gene duplication ancestral to the divergence of plants and animals gave rise to two main lineages of MADS-box genes: TypeI and TypeII. We locate the root of the eukaryotic MADS-box gene family between these two lineages. A novel monophyletic group of plant MADS domains (AGL34 like) seems to be more closely related to previously identified animal SRF-like MADS domains to form TypeI lineage. Most other plant sequences form a clear monophyletic group with animal MEF2-like domains to form TypeII lineage. Only plant TypeII members have a K domain that is downstream of the MADS domain in most plant members previously identified. This suggests that the K domain evolved after the duplication that gave rise to the two lineages. Finally, a group of intermediate plant sequences could be the result of recombination events. These analyses may guide the search for MADS-box sequences in basal eukaryotes and the phylogenetic placement of new genes from other plant species.
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Affiliation(s)
- E R Alvarez-Buylla
- Department of Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA.
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23
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Braun EL, Halpern AL, Nelson MA, Natvig DO. Large-scale comparison of fungal sequence information: mechanisms of innovation in Neurospora crassa and gene loss in Saccharomyces cerevisiae. Genome Res 2000; 10:416-30. [PMID: 10779483 DOI: 10.1101/gr.10.4.416] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We report a large-scale comparison of sequence data from the filamentous fungus Neurospora crassa with the complete genome sequence of Saccharomyces cerevisiae. N. crassa is considerably more morphologically and developmentally complex than S. cerevisiae. We found that N. crassa has a much higher proportion of "orphan" genes than S. cerevisiae, suggesting that its morphological complexity reflects the acquisition or maintenance of novel genes, consistent with its larger genome. Our results also indicate the loss of specific genes from S. cerevisiae. Surprisingly, some of the genes lost from S. cerevisiae are involved in basic cellular processes, including translation and ion (especially calcium) homeostasis. Horizontal gene transfer from prokaryotes appears to have played a relatively modest role in the evolution of the N. crassa genome. Differences in the overall rate of molecular evolution between N. crassa and S. cerevisiae were not detected. Our results indicate that the current public sequence databases have fairly complete samples of gene families with ancient conserved regions, suggesting that further sequencing will not substantially change the proportion of genes with homologs among distantly related groups. Models of the evolution of fungal genomes compatible with these results, and their functional implications, are discussed.
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Affiliation(s)
- E L Braun
- Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA
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24
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Kvint K, Hosbond C, Farewell A, Nybroe O, Nyström T. Emergency derepression: stringency allows RNA polymerase to override negative control by an active repressor. Mol Microbiol 2000; 35:435-43. [PMID: 10652104 DOI: 10.1046/j.1365-2958.2000.01714.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The uspA promoter, driving production of the universal stress protein A in response to diverse stresses, is demonstrated to be under dual control. One regulatory pathway involves activation of the promoter by the alarmone guanosine 3',5'-bisphosphate, via the beta-subunit of RNA polymerase, whereas the other consists of negative control by the FadR repressor. In contrast to canonical dual control by activation and repression circuits, which depends on concomitant activation and derepression for induction to occur, the ppGpp-dependent activation of the uspA promoter overrides repression by an active FadR under conditions of severe cellular stress (starvation). The ability of RNA polymerase to overcome repression during stringency depends, in part, on the strength of the FadR operator. This emergency derepression is operative on other FadR-regulated genes induced by starvation and is argued to be an essential regulatory mechanism operating during severe stress.
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Affiliation(s)
- K Kvint
- Department of Cell and Molecular Biology - Microbiology, Göteborg University, Box 462, 405 30 Göteborg, Sweden
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25
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Theissen G, Becker A, Di Rosa A, Kanno A, Kim JT, Münster T, Winter KU, Saedler H. A short history of MADS-box genes in plants. PLANT MOLECULAR BIOLOGY 2000; 42:115-149. [PMID: 10688133 DOI: 10.1023/a:1006332105728] [Citation(s) in RCA: 325] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Evolutionary developmental genetics (evodevotics) is a novel scientific endeavor which assumes that changes in developmental control genes are a major aspect of evolutionary changes in morphology. Understanding the phylogeny of developmental control genes may thus help us to understand the evolution of plant and animal form. The principles of evodevotics are exemplified by outlining the role of MADS-box genes in the evolution of plant reproductive structures. In extant eudicotyledonous flowering plants, MADS-box genes act as homeotic selector genes determining floral organ identity and as floral meristem identity genes. By reviewing current knowledge about MADS-box genes in ferns, gymnosperms and different types of angiosperms, we demonstrate that the phylogeny of MADS-box genes was strongly correlated with the origin and evolution of plant reproductive structures such as ovules and flowers. It seems likely, therefore, that changes in MADS-box gene structure, expression and function have been a major cause for innovations in reproductive development during land plant evolution, such as seed, flower and fruit formation.
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Affiliation(s)
- G Theissen
- Max-Planck-Institut für Züchtungsforschung, Abteilung Molekulare Pflanzengenetik, Köln, Germany
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26
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Kwok SF, Staub JM, Deng XW. Characterization of two subunits of Arabidopsis 19S proteasome regulatory complex and its possible interaction with the COP9 complex. J Mol Biol 1999; 285:85-95. [PMID: 9878390 DOI: 10.1006/jmbi.1998.2315] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The nuclear localized, multi-subunit COP9 complex (or COP9 signalosome) is a key developmental modulator involved in repression of photomorphogenesis. In an effort to further define the molecular actions of the COP9 complex, a yeast two hybrid interactive screen was undertaken to identify proteins that could directly interact with one subunit of this complex, namely FUS6/COP11. This screen identified one specific interactive protein, AtS9, that is likely the Arabidopsis non-ATPase S9 (subunit 9) of the 19S regulatory complex from the 26S proteasome. AtS9 specifically interacts with FUS6/COP11 via the C-terminal domain of FUS6/COP11, which is distinct from the N-terminal domain necessary for FUS6/COP11 to interact with itself. As anticipated, AtS9 is not a member of the COP9 complex, but tightly associates with an ATPase subunit of the Arabidopsis 19S proteasome regulatory complex, AtS6A. Since all three proteins, FUS6/COP11, AtS9, and AtS6A, are present as complexed forms in vivo, the observed interaction implies that the COP9 complex may directly interact with the 19S regulatory complex of the 26S proteasome or other potential AtS9-containing complex. This notion is consistent with the parallel tissue-specific expression patterns and the similar, predominantly nuclear localization of both the COP9 complex and the AtS9 protein.
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Affiliation(s)
- S F Kwok
- Department of Molecular Cellular, and Developmental Biology, Yale University, New Haven, CT, 06520-8104, USA
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Chan RL, Gago GM, Palena CM, Gonzalez DH. Homeoboxes in plant development. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1442:1-19. [PMID: 9767075 DOI: 10.1016/s0167-4781(98)00119-5] [Citation(s) in RCA: 153] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The homeobox is a 180 bp consensus DNA sequence present in a number of genes involved in developmental processes. This review focuses on the structure and function of plant homeobox genes and of the proteins they encode. Plant homeobox genes have been identified in studies using mutants, degenerate oligonucleotides deduced from conserved sequences, differential screening or binding to known promoters. According to sequence conservation, plant homeoboxes can be subdivided into different families, each comprising several members. Evolutionary studies indicate that the different families have diverged prior to the separation of the branches leading to animals, plants and fungi. Accordingly, members of different families show characteristic structural and functional properties. As an example, kn1-like genes seem to be involved in different aspects of the control of cell fate determination in the shoot meristem; HD-Zip genes, which encode proteins containing a leucine zipper motif adjacent to the homeodomain, are believed to operate at later stages of development; and gl2-like genes are involved in epidermal cell differentiation. Future studies should be oriented to discern the precise function of the many homeobox genes present in plant genomes, and to evaluate their use as modifiers of plant development.
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Affiliation(s)
- R L Chan
- Area Biología Molecular, Facultad de Ciencias Bioquímicas y Farmacéuticas (UNR) and Programa Multidisciplinario de Biología Experimental (PROMUBIE, CONICET), Suipacha 531, 2000 Rosario, Argentina
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Nyström T, Gustavsson N. Maintenance energy requirement: what is required for stasis survival of Escherichia coli? BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1365:225-31. [PMID: 9693738 DOI: 10.1016/s0005-2728(98)00072-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Little is known about how the energy of maintenance is generated in a cell supporting its persistence solely on endogenous carbon material, and what this energy is used for. However, it is clear that the endogenous metabolism of Escherichia coli cells held in the absence of exogenous carbon includes de novo protein synthesis, and that this synthesis is required for the maintenance of the growth-arrested cell. Recent findings suggest that several genes/proteins responding to carbon starvation are themselves involved in reorganizing and modulating catabolic flux, while others form an integral part of a defense system aimed at avoiding the damaging effects of ongoing respiratory activity. A significant fraction of the energy of maintenance is suggested to be required to prevent the denaturation and spontaneous aging of proteins during stasis.
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Affiliation(s)
- T Nyström
- Department of Microbiology, University of Lund, Sweden.
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Aravind L, Ponting CP. Homologues of 26S proteasome subunits are regulators of transcription and translation. Protein Sci 1998; 7:1250-4. [PMID: 9605331 PMCID: PMC2144014 DOI: 10.1002/pro.5560070521] [Citation(s) in RCA: 109] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Single copies of an alpha-helical-rich motif are demonstrated to be present within subunits of the large multiprotein 26S proteasome and eukaryotic initiation factor-3 (eIF3) complexes, and within proteins involved in transcriptional regulation. In addition, p40 and p47 subunits of eIF3 are shown to be homologues of the proteasome subunit Mov34, and transcriptional regulators JAB1/pad1. Finally, the proteasome subunit S5a and the p44 subunit of the basal transcription factor IIH (TFIIH) are identified as homologues. The presence of homologous, and sometimes identical, proteins in contrasting functional contexts suggests that the large multisubunit complexes of the 26S proteasome, eIF3 and TFIIH perform overlapping cellular roles.
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Affiliation(s)
- L Aravind
- Department of Biology-BSBW, Texas A&M University, College Station 77843, USA
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Andrade MA, Sander C, Valencia A. Updated catalogue of homologues to human disease-related proteins in the yeast genome. FEBS Lett 1998; 426:7-16. [PMID: 9598968 DOI: 10.1016/s0014-5793(98)00277-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The recent availability of the full Saccharomyces cerevisiae genome offers a perfect opportunity for revising the number of homologues to human disease-related proteins. We carried out automatic analysis of the complete S. cerevisiae genome and of the set of human disease-related proteins as identified in the SwissProt sequence data base. We identified 285 yeast proteins similar to 155 human disease-related proteins, including 239 possible cases of human-yeast direct functional equivalence (orthology). Of these, 40 cases are suggested as new, previously undiscovered relationships. Four of them are particularly interesting, since the yeast sequence is the most phylogenetically distant member of the protein family, including proteins related to diseases such as phenylketonuria, lupus erythematosus, Norum and fish eye disease and Wiskott-Aldrich syndrome.
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Affiliation(s)
- M A Andrade
- Protein Design Group, CNB-CSIC, Campus Universidad Autonoma, Cantoblanco, Madrid, Spain
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Kerstetter RA, Laudencia-Chingcuanco D, Smith LG, Hake S. Loss-of-function mutations in the maize homeobox gene, knotted1, are defective in shoot meristem maintenance. Development 1997; 124:3045-54. [PMID: 9272946 DOI: 10.1242/dev.124.16.3045] [Citation(s) in RCA: 158] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The product of the maize homeobox gene, knotted1 (kn1), localizes to the nuclei of cells in shoot meristems, but is absent from portions of the meristem where leaf primordia or floral organs initiate. Recessive mutant alleles of kn1 were obtained by screening for loss of the dominant leaf phenotype in maize. Mutant kn1 alleles carrying nonsense, splicing and frame shift mutations cause severe inflorescence and floral defects. Mutant tassels produce fewer branches and spikelets. Ears are often absent, and when present, are small with few spikelets. In addition, extra carpels form in female florets and ovule tissue proliferates abnormally. Less frequently, extra leaves form in the axils of vegetative leaves. These mutations reveal a role for kn1 in meristem maintenance, particularly as it affects branching and lateral organ formation.
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Affiliation(s)
- R A Kerstetter
- Plant and Microbial Biology Department, University of California, Berkeley 94720, USA
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Mushegian AR, Bassett DE, Boguski MS, Bork P, Koonin EV. Positionally cloned human disease genes: patterns of evolutionary conservation and functional motifs. Proc Natl Acad Sci U S A 1997; 94:5831-6. [PMID: 9159160 PMCID: PMC20866 DOI: 10.1073/pnas.94.11.5831] [Citation(s) in RCA: 177] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Positional cloning has already produced the sequences of more than 70 human genes associated with specific diseases. In addition to their medical importance, these genes are of interest as a set of human genes isolated solely on the basis of the phenotypic effect of the respective mutations. We analyzed the protein sequences encoded by the positionally cloned disease genes using an iterative strategy combining several sensitive computer methods. Comparisons to complete sequence databases and to separate databases of nematode, yeast, and bacterial proteins showed that for most of the disease gene products, statistically significant sequence similarities are detectable in each of the model organisms. Only the nematode genome encodes apparent orthologs with conserved domain architecture for the majority of the disease genes. In yeast and bacterial homologs, domain organization is typically not conserved, and sequence similarity is limited to individual domains. Generally, human genes complement mutations only in orthologous yeast genes. Most of the positionally cloned genes encode large proteins with several globular and nonglobular domains, the functions of some or all of which are not known. We detected conserved domains and motifs not described previously in a number of proteins encoded by disease genes and predicted functions for some of them. These predictions include an ATP-binding domain in the product of hereditary nonpolyposis colon cancer gene (a MutL homolog), which is conserved in the HS90 family of chaperone proteins, type II DNA topoisomerases, and histidine kinases, and a nuclease domain homologous to bacterial RNase D and the 3'-5' exonuclease domain of DNA polymerase I in the Werner syndrome gene product.
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Affiliation(s)
- A R Mushegian
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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