1
|
Arizala D, Dobhal S, Alvarez AM, Arif M. Elevation of Clavibacter michiganensis subsp. californiensis to species level as Clavibacter californiensis sp. nov., merging and re-classification of Clavibacter michiganensis subsp. chilensis and Clavibacter michiganensis subsp. phaseoli as Clavibacter phaseoli sp. nov. based on complete genome in silico analyses. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Gram-positive genus
Clavibacter
is currently divided into seven species (
Clavibacter michiganensis
,
Clavibacter nebraskensis
,
Clavibacter capsici
,
Clavibacter sepedonicus
,
Clavibacter tessellarius
,
Clavibacter insidiosus
and
Clavibacter zhangzhiyongii
) and three subspecies (
C. michiganensis
subsp.
californiensis
,
C. michiganensis
subsp.
chilensis
and
C. michiganensis
subsp.
phaseoli
). Recent studies have indicated that the taxonomic rank of the subspecies must be re-evaluated. In this research, we assessed the taxonomic position of the three
C. michiganensis
subspecies and clarified the taxonomic nomenclature of other 75
Clavibacter
strains. The complete genomes of the type strains of the three
Clavibacter
subspecies, the type strain of
C. tessellarius
and
C. nebraskensis
A6096 were sequenced using PacBio RSII technology. Application of whole-genome-based computational approaches such as average nucleotide identity (ANI), digital DNA–DNA hybridization, multi-locus sequence analysis of seven housekeeping genes (acnA, atpD, bipA, icdA, mtlD, recA and rpoB), a phylogenomic tree reconstructed from 1 028 core genes, and ANI-based phylogeny provided sufficient justification for raising
C. michiganensis
subsp.
californiensis
to the species level. These results led us to propose the establishment of Clavibacter californiensis sp. nov. as a species with its type strain C55T (=CFBP 8216T=ATCC BAA-2691T). Moreover, the orthologous and in silico dot plot analyses, along with the above described bioinformatic strategies, revealed a high degree of similarity between
C. michiganensis
subsp.
chilensis
and
C. michiganensis
subsp.
phaseoli
. Based on these analyses, we propose that both subspecies be combined into a single taxon and elevated to the species level as Clavibacter phaseoli sp. nov., with LPPA 982T (= CECT 8144T= LMG 27667T) as the type strain.
Collapse
Affiliation(s)
- Dario Arizala
- Department of Plant and Environmental Protection Sciences, University of Hawai'i at Manoa, Honolulu, HI 96822, USA
| | - Shefali Dobhal
- Department of Plant and Environmental Protection Sciences, University of Hawai'i at Manoa, Honolulu, HI 96822, USA
| | - Anne M. Alvarez
- Department of Plant and Environmental Protection Sciences, University of Hawai'i at Manoa, Honolulu, HI 96822, USA
| | - Mohammad Arif
- Department of Plant and Environmental Protection Sciences, University of Hawai'i at Manoa, Honolulu, HI 96822, USA
| |
Collapse
|
2
|
Cui X, Jun JH, Rao X, Bahr C, Chapman E, Temple S, Dixon RA. Leaf layer-based transcriptome profiling for discovery of epidermal-selective promoters in Medicago truncatula. PLANTA 2022; 256:31. [PMID: 35790623 DOI: 10.1007/s00425-022-03920-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
Transcriptomics of manually dissected leaf layers from Medicago truncatula identifies genes with preferential expression in upper and/or lower epidermis. The promoters of these genes confer epidermal-specific expression of transgenes. Improving the quality and quantity of proanthocyanidins (PAs) in forage legumes has potential to improve the nitrogen nutrition of ruminant animals and protect them from the risk of pasture bloat, as well as parasites. However, ectopic constitutive accumulation of PAs in plants by genetic engineering can significantly inhibit growth. We selected the leaf epidermis as a candidate tissue for targeted engineering of PAs or other pathways. To identify gene promoters selectively expressed in epidermal tissues, we performed comparative transcriptomic analyses in the model legume Medicago truncatula, using five tissue samples representing upper epidermis, lower epidermis, whole leaf without upper epidermis, whole leaf without lower epidermis, and whole leaf. We identified 52 transcripts preferentially expressed in upper epidermis, most of which encode genes involved in flavonoid biosynthesis, and 53 transcripts from lower epidermis, with the most enriched category being anatomical structure formation. Promoters of the preferentially expressed genes were cloned from the M. truncatula genome and shown to direct tissue-selective promoter activities in transient assays. Expression of the PA pathway transcription factor TaMYB14 under control of several of the promoters in transgenic alfalfa resulted in only modest MYB14 transcript accumulation and low levels of PA production. Activity of a subset of promoters was confirmed by transcript analysis in field-grown alfalfa plants throughout the growing season, and revealed variable but consistent expression, which was generally highest 3-4 weeks after cutting. We conclude that, although the selected promoters show acceptable tissue-specificity, they may not drive high enough transcription factor expression to activate the PA pathway.
Collapse
Affiliation(s)
- Xin Cui
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #311428, Denton, TX, 76203, USA
| | - Ji Hyung Jun
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #311428, Denton, TX, 76203, USA
- Children's Research Institute and the Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Xiaolan Rao
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #311428, Denton, TX, 76203, USA
- College of Life Sciences, Hubei University, Wuhan, 430068, Hubei, China
| | - Camille Bahr
- Forage Genetics International, N5292 Gills Coulee Rd S, West Salem, WI, 54669, USA
| | - Elisabeth Chapman
- Forage Genetics International, N5292 Gills Coulee Rd S, West Salem, WI, 54669, USA
| | - Stephen Temple
- Forage Genetics International, N5292 Gills Coulee Rd S, West Salem, WI, 54669, USA
| | - Richard A Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #311428, Denton, TX, 76203, USA.
| |
Collapse
|
3
|
Osdaghi E, van der Wolf JM, Abachi H, Li X, De Boer S, Ishimaru CA. Bacterial ring rot of potato caused by Clavibacter sepedonicus: A successful example of defeating the enemy under international regulations. MOLECULAR PLANT PATHOLOGY 2022; 23:911-932. [PMID: 35142424 PMCID: PMC9190974 DOI: 10.1111/mpp.13191] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 05/03/2023]
Abstract
BACKGROUND Bacterial ring rot of potato (Solanum tuberosum) caused by the gram-positive coryneform bacterium Clavibacter sepedonicus is an important quarantine disease threatening the potato industry around the globe. Since its original description in 1906 in Germany, management of ring rot has been a major problem due to the seedborne nature (via seed tubers not true seeds) of the pathogen allowing the bacterium to be transmitted long distances via infected tubers. DISEASE SYMPTOMS On growing potato plants: interveinal chlorosis on leaflets leading to necrotic areas and systemic wilt. On infected tubers: vascular tissues become yellowish brown with a cheesy texture due to bacterial colonization and decay. HOST RANGE Potato is the main host of the pathogen, but natural infection also occurs on eggplant, tomato, and sugar beet. TAXONOMIC STATUS OF THE PATHOGEN Class: Actinobacteria; Order: Actinomycetales; Family: Microbacteriaceae; Genus: Clavibacter; Species: Clavibacter sepedonicus (Spieckermann and Kotthoff 1914) Li et al. 2018. SYNONYMS (NONPREFERRED SCIENTIFIC NAMES) Aplanobacter sepedonicus; Bacterium sepedonicum; Corynebacterium sepedonicum; Corynebacterium michiganense pv. sepedonicum; Clavibacter michiganensis subsp. sepedonicus. MICROBIOLOGICAL PROPERTIES Gram-positive, club-shaped cells with creamy to yellowish-cream colonies for which the optimal growth temperature is 20-23°C. DISTRIBUTION Asia (China, Japan, Kazakhstan, Nepal, North Korea, Pakistan, South Korea, Uzbekistan, the Asian part of Russia), Europe (Belarus, Bulgaria, Czech Republic, Estonia, Finland, Georgia, Germany, Greece, Hungary, Latvia, Lithuania, Norway, Poland, Romania, European part of Russia, Slovakia, Spain, Sweden, Turkey, Ukraine), and North America (Canada, Mexico, USA). PHYTOSANITARY CATEGORIZATION CORBSE: EPPO A2 list no. 51. EU; Annex designation I/A2.
Collapse
Affiliation(s)
- Ebrahim Osdaghi
- Department of Plant ProtectionCollege of AgricultureUniversity of TehranKarajIran
| | - Jan M. van der Wolf
- Business Unit Biointeractions and Plant HealthWageningen University and ResearchWageningenNetherlands
| | - Hamid Abachi
- Department of Plant ProtectionCollege of AgricultureUniversity of TehranKarajIran
| | - Xiang Li
- Canadian Food Inspection Agency, Charlottetown LaboratoryCharlottetownPECanada
| | - Solke H. De Boer
- Canadian Food Inspection Agency, Charlottetown LaboratoryCharlottetownPECanada
| | | |
Collapse
|
4
|
Stevens DM, Tang A, Coaker G. A Genetic Toolkit for Investigating Clavibacter Species: Markerless Deletion, Permissive Site Identification, and an Integrative Plasmid. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1336-1345. [PMID: 34890250 DOI: 10.1094/mpmi-07-21-0171-ta] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The development of knockout mutants and expression variants are critical for understanding genotype-phenotype relationships. However, advances in these techniques in gram-positive actinobacteria have stagnated over the last decade. Actinobacteria in the Clavibacter genus are composed of diverse crop pathogens that cause a variety of wilt and cankering diseases. Here, we present a suite of tools for genetic manipulation in the tomato pathogen Clavibacter michiganensis including a markerless deletion system, an integrative plasmid, and an R package for identification of permissive sites for plasmid integration. The vector pSelAct-KO is a recombination-based, markerless knockout system that uses dual selection to engineer seamless deletions of a region of interest, providing opportunities for repeated higher-order genetic knockouts. The efficacy of pSelAct-KO was demonstrated in C. michiganensis and was confirmed using whole-genome sequencing. We developed permissR, an R package to identify permissive sites for chromosomal integration, which can be used in conjunction with pSelAct-Express, a nonreplicating integrative plasmid that enables recombination into a permissive genomic location. Expression of enhanced green fluorescent protein by pSelAct-Express was verified in two candidate permissive regions predicted by permissR in C. michiganensis. These molecular tools are essential advances for investigating gram-positive actinobacteria, particularly for important pathogens in the Clavibacter genus.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Collapse
Affiliation(s)
- Danielle M Stevens
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, Davis, CA 95616, U.S.A
- Department of Plant Pathology, University of California, Davis, Davis, CA 95616, U.S.A
| | - Andrea Tang
- Department of Plant Pathology, University of California, Davis, Davis, CA 95616, U.S.A
| | - Gitta Coaker
- Department of Plant Pathology, University of California, Davis, Davis, CA 95616, U.S.A
| |
Collapse
|
5
|
Hwang IS, Lee HM, Oh E, Lee S, Heu S, Oh C. Plasmid composition and the chpG gene determine the virulence level of Clavibacter capsici natural isolates in pepper. MOLECULAR PLANT PATHOLOGY 2020; 21:808-819. [PMID: 32196887 PMCID: PMC7214350 DOI: 10.1111/mpp.12932] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 02/21/2020] [Accepted: 02/22/2020] [Indexed: 05/23/2023]
Abstract
The gram-positive bacterial species Clavibacter capsici causes necrosis and canker in pepper plants. Genomic and functional analyses of C. capsici type strain PF008 have shown that multiple virulence genes exist in its two plasmids. We aimed to identify the key determinants that control the virulence of C. capsici. Pepper leaves inoculated with 54 natural isolates exhibited significant variation in the necrosis. Six isolates showed very low virulence, but their population titres in plants were not significantly different from those of the highly virulent isolates. All six isolates lacked the pCM1Cc plasmid that carries chpG, which has been shown to be required for virulence and encodes a putative serine protease, but two of them, isolates 1,106 and 1,207, had the intact chpG elsewhere in the genome. Genomic analysis of these two isolates revealed that chpG was located in the pCM2Cc plasmid, and two highly homologous regions were present next to the chpG locus. The chpG expression in isolate 1,106 was not induced in plants. Introduction of chpG of the PF008 strain into the six low-virulence isolates restored their virulence to that of PF008. Our findings indicate that there are at least three different variant groups of C. capsici and that the plasmid composition and the chpG gene are critical for determining the virulence level. Moreover, our findings also indicate that the virulence level of C. capsici does not directly correlate with bacterial titres in plants.
Collapse
Affiliation(s)
- In Sun Hwang
- Department of Horticultural BiotechnologyCollege of Life SciencesKyung Hee UniversityYonginSouth Korea
| | - Hyo Min Lee
- Department of Horticultural BiotechnologyCollege of Life SciencesKyung Hee UniversityYonginSouth Korea
| | - Eom‐Ji Oh
- Department of Horticultural BiotechnologyCollege of Life SciencesKyung Hee UniversityYonginSouth Korea
| | - Seungdon Lee
- Planning and Coordination DivisionNational Institute of Agricultural SciencesRural Development AdministrationWanjuSouth Korea
| | - Sunggi Heu
- Crop Cultivation and Environment Research DivisionNational Institute of Crop ScienceRural Development AdministrationSuwonSouth Korea
| | - Chang‐Sik Oh
- Department of Horticultural BiotechnologyCollege of Life SciencesKyung Hee UniversityYonginSouth Korea
| |
Collapse
|
6
|
Owusu V, Mira M, Soliman A, Adam LR, Daayf F, Hill RD, Stasolla C. Suppression of the maize phytoglobin ZmPgb1.1 promotes plant tolerance against Clavibacter nebraskensis. PLANTA 2019; 250:1803-1818. [PMID: 31456046 DOI: 10.1007/s00425-019-03263-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 08/16/2019] [Indexed: 06/10/2023]
Abstract
Suppression of the maize phytoglobin ZmPgb1.1 enhances tolerance against Clavibacter nebraskensis by promoting hypersensitive response mechanisms mediated by ethylene and reactive oxygen species. Suppression of the maize phytoglobin, ZmPgb1.1, reduced lesion size and disease severity in leaves following inoculation with Clavibacter nebraskensis, the causal agent of Goss's bacterial wilt disease of corn. These effects were associated with an increase of the transcriptional levels of ethylene biosynthetic and responsive genes, which resulted in the accumulation of reactive oxygen species (ROS) and TUNEL-positive nuclei in the proximity of the inoculation site. An in vitro system, in which maize cells were treated with induced xylem sap, was employed to define the cause-effect relationship of these events. Phytoglobins (Pgbs) are hemoglobins able to scavenge nitric oxide (NO). Suppression of ZmPgb1.1 elevated the level of NO in cells exposed to the induced xylem sap causing a rise in the transcript levels of ethylene biosynthesis and response genes, as well as ethylene. Accumulation of ethylene in the same cells was sufficient to elevate the amount of reactive oxygen species (ROS), through the activation of the respiratory burst oxidase homologs (Rboh) genes, and trigger programmed cell death (PCD). The sequence of these events was demonstrated by manipulating the content of NO and ethylene in culture through pharmacological treatments. Collectively, our results illustrated that suppression of ZmPgb1.1 evokes tolerance against C. nebraskensis culminating in the execution of PCD, a key step of the hypersensitive response.
Collapse
Affiliation(s)
- V Owusu
- Department of Plant Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - M Mira
- Department of Botany, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - A Soliman
- Department of Genetics, Faculty of Agriculture, Tanta University, Tanta, Egypt
| | - L R Adam
- Department of Plant Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - F Daayf
- Department of Plant Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - R D Hill
- Department of Plant Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - C Stasolla
- Department of Plant Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.
| |
Collapse
|
7
|
Thapa SP, Davis EW, Lyu Q, Weisberg AJ, Stevens DM, Clarke CR, Coaker G, Chang JH. The Evolution, Ecology, and Mechanisms of Infection by Gram-Positive, Plant-Associated Bacteria. ANNUAL REVIEW OF PHYTOPATHOLOGY 2019; 57:341-365. [PMID: 31283433 DOI: 10.1146/annurev-phyto-082718-100124] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Gram-positive bacteria are prominent members of plant-associated microbial communities. Although many are hypothesized to be beneficial, some are causative agents of economically important diseases of crop plants. Because the features of Gram-positive bacteria are fundamentally different relative to those of Gram-negative bacteria, the evolution and ecology as well as the mechanisms used to colonize and infect plants also differ. Here, we discuss recent advances in our understanding of Gram-positive, plant-associated bacteria and provide a framework for future research directions on these important plant symbionts.
Collapse
Affiliation(s)
- Shree P Thapa
- Department of Plant Pathology, University of California, Davis, California 95616, USA
| | - Edward W Davis
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA;
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon 97331, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USA
| | - Qingyang Lyu
- Department of Plant Pathology, University of California, Davis, California 95616, USA
| | - Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA;
| | - Danielle M Stevens
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA;
- Integrative Genetics and Genomics, University of California, Davis, California 95616, USA
| | - Christopher R Clarke
- Genetic Improvement for Fruits and Vegetables Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, Maryland 20705, USA
| | - Gitta Coaker
- Department of Plant Pathology, University of California, Davis, California 95616, USA
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA;
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon 97331, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USA
| |
Collapse
|