Genome Annotation of a Model Diatom Phaeodactylum tricornutum Using an Integrated Proteogenomic Pipeline

Effect of RNA Demethylase FTO Overexpression on Biomass and Bioactive Substances in Diatom Phaeodactylum tricornutum

Phaeodactylum tricornutum is rich in bioactive substances, rendering it valuable in nutrition and medicine. Epigenetic editing mediated by human RNA demethylase FTO can significantly increase the yields of rice and potato and offers significant potential for the genetic breeding of microalgae. This study aimed to enhance the production of certain metabolites in P. tricornutum via FTO-mediated epigenetic editing. Phenotypic analysis revealed that transgenic P. tricornutum exhibits significantly reduced RNA m6A modification levels and faster growth, producing markedly higher levels of lipids, proteins, and carotenoids than the wild type. Transcriptome analysis revealed 1009 upregulated genes and 378 downregulated genes. KEGG analysis demonstrated the upregulated expression of multiple key enzymes involved in long-chain fatty acid synthesis (e.g., ACSL, fabF, and fabG), carotenoid synthesis (e.g., crtQ, PDS, and PSY1), and amino acid synthesis (e.g., dapF, glyA, and aroK) in transgenic P. tricornutum, consistent with our phenotypic results. These results indicate that FTO can promote growth and increase the bioactive compound content in P. tricornutum by regulating the m6A modification of RNA, and further suggest that FTO has the potential to serve as a new tool for the epigenetic editing of microalgae.

Proteogenomic analysis of Cyprinid herpesvirus 2 using high-resolution mass spectrometry

Cyprinid herpesvirus 2 (CyHV-2) is the main pathogen responsible for the development of herpesviral hematopoietic necrosis disease (HVHND) in crucian carp (Carassius auratus). The CyHV-2 genome encodes approximately 150 genes that are expressed in a well-defined manner during productive infection. However, CyHV-2 open reading frames (ORFs) are primarily derived from sequence and homology analyses, and most lack protein-level evidence to support their properties. In this study, we used high-resolution mass spectrometry followed by proteogenomic mapping to achieve genome re-annotation of CyHV-2. Based on our results, a total of 1,683 MS/MS spectra could be mapped to the CyHV-2 genome through six-frame translation, with 1,665 corresponding to 117 currently annotated protein-coding ORFs. Three of the remaining 18 peptides were mapped to the N-terminal extension region of known ORFs. However, 12 novel CyHV-2 ORFs, designated nORF1-12, were identified and characterized for the first time based on the remaining 15 peptides that could be mapped to previously unannotated regions of the viral genome. And the sequence differences of the novel phosphorylated nORF1, also referred to as ORF25E, in different CyHV-2 strains indicated that the nORF1 is a prospective molecular marker that can monitor the evolution from the Japan (J) to the China (C) genotype of CyHV-2. These findings further validate existing annotations, expand the genomic landscape of CyHV-2, and provide a rich resource for aquatic virology research.IMPORTANCECyHV-2 is a viral pathogen that poses a significant threat to crucian carp farming. CyHV-2 has a large genome with complex sequence features and diverse coding mechanisms, which complicates accurate genome annotation in the absence of protein-level evidence. Here, we employed various protein extraction and separation methods to increase viral protein coverage and performed an integrated proteogenomic analysis to refine the CyHV-2 genome annotation. A total of 129 viral genes were confidently identified, including 117 currently annotated genes and 12 novel genes. For the first time, we present large-scale evidence of peptide presence and levels in the genome of aquatic viruses and confirm the majority of the predicted proteins in CyHV-2. Our findings enhance the understanding of the CyHV-2 genome structure and provide valuable insights for future studies on CyHV-2 biology.

Localization of heme biosynthesis in the diatom Phaeodactylum tricornutum and differential expression of multi-copy enzymes

Heme is essential for all organisms. The composition and location of the pathway for heme biosynthesis, have been influenced by past endosymbiotic events and organelle evolution in eukaryotes. Endosymbioses led to temporary redundancy of the enzymes and the genes involved. Genes were transferred to the nucleus from different endosymbiotic partners, and their multiple copies were either lost or retained, resulting in a mosaic pathway. This mosaic is particularly complex in organisms with eukaryote-derived plastids, such as diatoms. The plastids of diatoms are clearly derived from red algae. However, it is not entirely clear whether they were acquired directly from a red algal ancestor or indirectly in higher-order endosymbioses. In the diatom Phaeodactylum tricornutum, most enzymes of the pathway are present in a single copy, but three, glutamyl-tRNA synthetase (GluRS), uroporphyrinogen decarboxylase (UROD) and coproporphyrinogen oxidase (CPOX), are encoded in multiple copies. These are not direct paralogs resulting from gene duplication within the lineage but were acquired horizontally during the plastid endosymbioses. While some iso-enzymes originate from the host cell, others originate either from the genome of the cyanobacterial ancestor of all plastids or from the nuclear genome of the eukaryotic ancestor of the diatom complex plastid, a rhodophyte or an alga containing rhodophyte-derived plastids, a situation known as pseudoparalogy. Using green fluorescent protein-tagged expression and immunogold labeling, we experimentally localized all enzymes of the pathway in P. tricornutum, and confirmed their localization in the plastid, with a few possible exceptions. Our meta-analyses of transcription data showed that the pseudoparalogs are differentially expressed in response to nitrate starvation, blue light, high light, high CO2, and the cell cycle. Taken together, our findings emphasize that the evolution of complex plastids via endosymbiosis has a direct impact not only on the genetics but also on the physiology of resulting organisms.

DiatOmicBase: a versatile gene-centered platform for mining functional omics data in diatom research

Diatoms are prominent microalgae found in all aquatic environments. Over the last 20 years, thanks to the availability of genomic and genetic resources, diatom species such as Phaeodactylum tricornutum and Thalassiosira pseudonana have emerged as valuable experimental model systems for exploring topics ranging from evolution to cell biology, (eco)physiology, and biotechnology. Since the first genome sequencing projects initiated more than 20 years ago, numerous genome-enabled datasets have been generated, based on RNA-Seq and proteomics experiments, epigenomes, and ecotype variant analysis. Unfortunately, these resources, generated by various laboratories, are often in disparate formats and challenging to access and analyze. Here we present DiatOmicBase, a genome portal gathering comprehensive omics resources from P. tricornutum and T. pseudonana to facilitate the exploration of dispersed public datasets and the design of new experiments based on the prior-art. DiatOmicBase provides gene annotations, transcriptomic profiles and a genome browser with ecotype variants, histone and methylation marks, transposable elements, non-coding RNAs, and read densities from RNA-Seq experiments. We developed a semi-automatically updated transcriptomic module to explore both publicly available RNA-Seq experiments and users' private datasets. Using gene-level expression data, users can perform exploratory data analysis, differential expression, pathway analysis, biclustering, and co-expression network analysis. Users can create heatmaps to visualize pre-computed comparisons for selected gene subsets. Automatic access to other bioinformatic resources and tools for diatom comparative and functional genomics is also provided. Focusing on the resources currently centralized for P. tricornutum, we showcase several examples of how DiatOmicBase strengthens molecular research on diatoms, making these organisms accessible to a broad research community.

Identification of Cocconeis neothumensis var. marina using a polyphasic approach including ultrastructure and gene annotation

Several microalgae, including marine diatoms, significantly contribute to the global primary production and play a vital role in the food webs of benthic and planktonic ecosystems. Diatoms of the genus Cocconeis frequently inhabit benthic substrates, including the leaves of seagrasses. They are seasonally dominant in the leaf epiphytic layer of the Mediterranean seagrass Posidonia oceanica L. Delile, and have been proposed as model organisms for chemical ecology studies. However, the genome of Cocconeis spp. has not been sequenced. Consequently, their low-level molecular identification is currently impossible, besides a few examples. To address this gap, a polyphasic identification of C. neothumensis has been employed, combining ultra-morphological data with DNA barcoding markers. A strain of diatoms was isolated from P. oceanica leaves. It has been cultured in the laboratory and examined under Scanning Electron Microscopy (SEM). The 18S ribosomal RNA gene (18S rRNA, nrDNA) and the ribulose 1,5-biphosphate carboxylase (rbcL, cpDNA) gene were analysed for DNA barcoding characterisation. Since ultra-morphology data unambiguously identified the isolated strain as C. neothumensis Krammer, 1991, the molecular sequences herein reported will facilitate its rapid and accurate identification. In addition, our comparative analyses will facilitate the evaluation of these molecular markers for identification of closely related benthic diatoms.

Aromatic Amino Acids: Exploring Microalgae as a Potential Biofactory

In recent times, microalgae have emerged as powerful hosts for biotechnological applications, ranging from the production of lipids and specialized metabolites (SMs) of pharmaceutical interest to biofuels, nutraceutical supplements, and more. SM synthesis through bioengineered pathways relies on the availability of aromatic amino acids (AAAs) as an essential precursor. AAAs, phenylalanine, tyrosine, and tryptophan are also the building blocks of proteins, maintaining the structural and functional integrity of cells. Hence, they are crucial intermediates linking the primary and specialized metabolism. The biosynthesis pathway of AAAs in microbes and plants has been studied for decades, but not much is known about microalgae. The allosteric control present in this pathway has been targeted for metabolic engineering in microbes. This review focuses on the biosynthesis of AAAs in eukaryotic microalgae and engineering techniques for enhanced production. All the putative genes involved in AAA pathways in the model microalgae Chlamydomonas reinhardtii and Phaeodactylum tricornutum are listed in this review.

Identification of Proteoforms Related to Nelumbo nucifera Flower Petaloid Through Proteogenomic Strategy

Nelumbo nucifera is an aquatic plant with a high ornamental value due to its flower. Despite the release of several versions of the lotus genome, its annotation remains inefficient, which makes it difficult to obtain a more comprehensive knowledge when -omic studies are applied to understand the different biological processes. Focusing on the petaloid of the lotus flower, we conducted a comparative proteomic analysis among five major floral organs. The proteogenomic strategy was applied to analyze the mass spectrometry data in order to dig out novel proteoforms that are involved in the petaloids of the lotus flower. The results revealed that a total of 4863 proteins corresponding to novel genes were identified, with 227 containing single amino acid variants (SAAVs), and 72 originating from alternative splicing (AS) genes. In addition, a range of post-translational modifications (PTMs) events were also identified in lotus. Through functional annotation and homology analysis with 24 closely related plant species, we identified five candidate proteins associated with floral organ development, which were not identified by ordinary proteomic analysis. This study not only provides new insights into understanding the mechanism of petaloids in lotus but is also helpful in identifying new proteoforms to improve the annotation of the lotus genome.

Comparative proteomic analysis of seed germination between allotetraploid cotton Gossypium hirsutum and Gossypium barbadense

Seed germination, a key initial event in the plant life cycle, directly affects cotton yield and quality. Gossypium barbadense and Gossypium hirsutum gradually evolved through polyploidization, resulting in different characteristics, and this interspecific variation lacks genetic and molecular explanation. This work aimed to compare the proteomes between G. barbadense and G. hirsutum during seed germination. Here, we identified 2740 proteins for G. barbadense and 3758 for G. hirsutum. In the initial state, proteins in two cotton involved similar bioprocess, such as sugar metabolism, DNA repairing, and ABA signaling pathway. However, in the post-germination stage, G. hirsutum expressed more protein related to redox homeostasis, peroxidase activity, and pathogen interactions. Analyzing the different expression patterns of 915 single-copy orthogroups between the two kinds of cotton indicated that most of the differentially expressed proteins in G. barbadense were related to carbon metabolism. In contrast, most proteins in G. hirsutum were associated with stress response. Besides that, by proteogenomic analysis, we found 349 putative non-canonical peptides, which may be involved in plant development. These results will help to understand the different characteristics of these two kinds of cotton, such as fiber quality, yield, and adaptability. SIGNIFICANCE STATEMENT: Cotton is the predominant natural fiber crop worldwide; Gossypium barbadense and Gossypium hirsutum have evolved through polyploidization to produce differing traits. However, given their specific features, the divergence of mechanisms underlying seed germination between G. hirsutum and G. barbadense has not been discussed. Here, we explore what protein contributes to interspecific differences between G. barbadense and G. hirsutum during the seed germination period. This study helps to elucidate the evolution and domestication history of cotton polyploids and may allow breeders to understand their domestication history better and improve fiber quality and adaptability.

Proteomics reveals the significance of vacuole Pi transporter in the adaptability of Brassica napus to Pi deprivation

Vacuolar Pi transporters (VPTs) have recently been identified as important regulators of cellular Pi status in Arabidopsis thaliana and Oryza sativa. In the oil crop Brassica napus, BnA09PHT5;1a and BnC09PHT5;1a are two homologs of AtPHT5;1, the vacuolar Pi influx transporter in Arabidopsis. Here, we show that Pi deficiency induces the transcription of both homologs of PHT5;1a genes in B. napus leaves. Brassica PHT5;1a double mutants (DM) had smaller shoots and higher cellular Pi concentrations than wild-type (WT, Westar 10), suggesting the potential role of BnPHT5;1a in modulating cellular Pi status in B. napus. A proteomic analysis was performed to estimate the role of BnPHT5;1a in Pi fluctuation. Results show that Pi deprivation disturbs the abundance of proteins in the physiological processes involved in carbohydrate metabolism, response to stimulus and stress in B. napus, while disruption of BnPHT5;1a genes may exacerbate these processes. Besides, the processes of cell redox homeostasis, lipid metabolic and proton transmembrane transport are supposed to be unbalanced in BnPHT5;1a DM under the -Pi condition. Noteworthy, disruption of BnPHT5;1a genes severely alters the abundance of proteins related to ATP biosynthesis, and proton/inorganic cation transmembrane under normal Pi condition, which might contribute to B. napus growth limitations. Additionally, seven new protein markers of Pi homeostasis are identified in B. napus. Taken together, this study characterizes the important regulatory role of BnPHT5;1a genes as vacuolar Pi influx transporters in Pi homeostasis in B. napus.

Proteomes reveal the lipid metabolic network in the complex plastid of Phaeodactylum tricornutum

Phaeodactylum tricornutum plastid is surrounded by four membranes, and its protein composition and function remain mysterious. In this study, the P. tricornutum plastid-enriched fraction was obtained and 2850 proteins were identified, including 92 plastid-encoded proteins, through label-free quantitative proteomic technology. Among them, 839 nuclear-encoded proteins were further determined to be plastidial proteins based on the BLAST alignments within Plant Proteome DataBase and subcellular localization prediction, in spite of the strong contamination by mitochondria-encoded proteins and putative plasma membrane proteins. According to our proteomic data, we reconstructed the metabolic pathways and highlighted the hybrid nature of this diatom plastid. Triacylglycerol (TAG) hydrolysis and glycolysis, as well as photosynthesis, glycan metabolism, and tocopherol and triterpene biosynthesis, occur in the plastid. In addition, the synthesis of long-chain acyl-CoAs, elongation, and desaturation of fatty acids (FAs), and synthesis of lipids including TAG are confined in the four-layered-membrane plastid based on the proteomic and GFP-fusion localization data. The whole process of generation of docosahexaenoic acid (22:6) from palmitic acid (16:0), via elongation and desaturation of FAs, occurs in the chloroplast endoplasmic reticulum membrane, the outermost membrane of the plastid. Desaturation that generates 16:4 from 16:0 occurs in the plastid stroma and outer envelope membrane. Quantitative analysis of glycerolipids between whole cells and isolated plastids shows similar composition, and the FA profile of TAG was not different. This study shows that the diatom plastid combines functions usually separated in photosynthetic eukaryotes, and differs from green alga and plant chloroplasts by undertaking the whole process of lipid biosynthesis.

Proteogenomics-based functional genome research: approaches, applications, and perspectives in plants

Proteogenomics (PG) integrates the proteome with the genome and transcriptome to refine gene models and annotation. Coupled with single-cell (SC) assays, PG effectively distinguishes heterogeneity among cell groups. Affiliating spatial information to PG reveals the high-resolution circuitry within SC atlases. Additionally, PG can investigate dynamic changes in protein-coding genes in plants across growth and development as well as stress and external stimulation, significantly contributing to the functional genome. Here we summarize existing PG research in plants and introduce the technical features of various methods. Combining PG with other omics, such as metabolomics and peptidomics, can offer even deeper insights into gene functions. We argue that the application of PG will represent an important font of foundational knowledge for plants.

A large-scale proteogenomic atlas of pear

Pear is an important fruit tree that is widely distributed around the world. The first pear genome map was reported from our laboratory approximately 10 years ago. To further study global protein expression patterns in pear, we generated pear proteome data based on 24 major tissues. The tissue-resolved profiles provided evidence of the expression of 17 953 proteins. We identified 4294 new coding events and improved the pear genome annotation via the proteogenomic strategy based on 18 090 peptide spectra with peptide spectrum matches >1. Among the eight randomly selected new short coding open reading frames that were expressed in the style, four promoted and one inhibited the growth of pear pollen tubes. Based on gene coexpression module analysis, we explored the key genes associated with important agronomic traits, such as stone cell formation in fruits. The network regulating the synthesis of lignin, a major component of stone cells, was reconstructed, and receptor-like kinases were implicated as core factors in this regulatory network. Moreover, we constructed the online database PearEXP (http://www.peardb.org.cn) to enable access to the pear proteogenomic resources. This study provides a paradigm for in-depth proteogenomic studies of woody plants.

Giant proteins in a giant cell: Molecular basis of ultrafast Ca2+-dependent cell contraction

The giant single-celled eukaryote, Spirostomum, exhibits one of the fastest movements in the biological world. This ultrafast contraction is dependent on Ca²⁺ rather than ATP and therefore differs to the actin-myosin system in muscle. We obtained the high-quality genome of Spirostomum minus from which we identified the key molecular components of its contractile apparatus, including two major Ca²⁺ binding proteins (Spasmin 1 and 2) and two giant proteins (GSBP1 and GSBP2), which act as the backbone and allow for the binding of hundreds of spasmins. The evidence suggests that the GSBP-spasmin protein complex is the functional unit of the mesh-like contractile fibrillar system, which, coupled with various other subcellular structures, provides the mechanism for repetitive ultrafast cell contraction and extension. These findings improve our understanding of the Ca²⁺-dependent ultrafast movement and provide a blueprint for future biomimicry, design, and construction of this kind of micromachine.

Improving the genome and proteome annotations of the marine model diatom Thalassiosira pseudonana using a proteogenomics strategy

Diatoms are unicellular eukaryotic phytoplankton that account for approximately 20% of global carbon fixation and 40% of marine primary productivity; thus, they are essential for global carbon biogeochemical cycling and climate. The availability of ten diatom genome sequences has facilitated evolutionary, biological and ecological research over the past decade; however, a complimentary map of the diatom proteome with direct measurements of proteins and peptides is still lacking. Here, we present a proteome map of the model marine diatom Thalassiosira pseudonana using high-resolution mass spectrometry combined with a proteogenomic strategy. In-depth proteomic profiling of three different growth phases and three nutrient-deficient samples identified 9526 proteins, accounting for ~ 81% of the predicted protein-coding genes. Proteogenomic analysis identified 1235 novel genes, 975 revised genes, 104 splice variants and 234 single amino acid variants. Furthermore, our quantitative proteomic analysis experimentally demonstrated that a considerable number of novel genes were differentially translated under different nutrient conditions. These findings substantially improve the genome annotation of T. pseudonana and provide insights into new biological functions of diatoms. This relatively comprehensive diatom proteome catalog will complement available diatom genome and transcriptome data to advance biological and ecological research of marine diatoms.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-022-00161-y.

A metabolic, phylogenomic and environmental atlas of diatom plastid transporters from the model species Phaeodactylum

Diatoms are an important group of algae, contributing nearly 40% of total marine photosynthetic activity. However, the specific molecular agents and transporters underpinning the metabolic efficiency of the diatom plastid remain to be revealed. We performed in silico analyses of 70 predicted plastid transporters identified by genome-wide searches of Phaeodactylum tricornutum. We considered similarity with Arabidopsis thaliana plastid transporters, transcriptional co-regulation with genes encoding core plastid metabolic pathways and with genes encoded in the mitochondrial genomes, inferred evolutionary histories using single-gene phylogeny, and environmental expression trends using Tara Oceans meta-transcriptomics and meta-genomes data. Our data reveal diatoms conserve some of the ion, nucleotide and sugar plastid transporters associated with plants, such as non-specific triose phosphate transporters implicated in the transport of phosphorylated sugars, NTP/NDP and cation exchange transporters. However, our data also highlight the presence of diatom-specific transporter functions, such as carbon and amino acid transporters implicated in intricate plastid-mitochondria crosstalk events. These confirm previous observations that substrate non-specific triose phosphate transporters (TPT) may exist as principal transporters of phosphorylated sugars into and out of the diatom plastid, alongside suggesting probable agents of NTP exchange. Carbon and amino acid transport may be related to intricate metabolic plastid-mitochondria crosstalk. We additionally provide evidence from environmental meta-transcriptomic/meta- genomic data that plastid transporters may underpin diatom sensitivity to ocean warming, and identify a diatom plastid transporter (J43171) whose expression may be positively correlated with temperature.

Large-scale discovery of non-conventional peptides in grape (Vitis vinifera L.) through peptidogenomics

Non-conventional peptides (NCPs), which are peptides derived from previously unannotated coding sequences, play important biological roles in plants. In this study, we used peptidogenomic methods that integrated mass spectrometry (MS) peptidomics and a six-frame translation database to extensively identify NCPs in grape. In total, 188 and 2021 non-redundant peptides from the Arabidopsis thaliana and Vitis vinifera L. protein database at Ensembl/URGI and an individualized peptidogenomic database were identified. Unlike conventional peptides, these NCPs derived mainly from intergenic, intronic, upstream ORF, 5'UTR, 3'UTR, and downstream ORF regions. These results show that unannotated regions are translated more broadly than we thought. We also found that most NCPs were derived from regions related to phenotypic variations, LTR retrotransposons, and domestication selection, indicating that the NCPs have an important function in complex biological processes. We also found that the NCPs were developmentally specific and had transient and specific functions in grape berry development. In summary, our study is the first to extensively identify NCPs in grape. It demonstrated that there was a large amount of translation in the genome. These results lay a foundation for studying the functions of NCPs and also provide a reference for the discovery of new functional genes in grape.

Decabromodiphenyl Ethane Mainly Affected the Muscle Contraction and Reproductive Endocrine System in Female Adult Zebrafish

The novel brominated flame retardant decabromodiphenyl ethane (DBDPE) has become a widespread environmental pollutant. However, the target tissue and toxicity of DBDPE are still not clear. In the current study, female zebrafish were exposed to 1 and 100 nM DBDPE for 28 days. Chemical analysis revealed that DBDPE tended to accumulate in the brain other than the liver and gonad. Subsequently, tandem mass tag-based quantitative proteomics and parallel reaction monitoring verification were performed to screen the differentially expressed proteins in the brain. Bioinformatics analysis revealed that DBDPE mainly affected the biological process related to muscle contraction and estrogenic response. Therefore, the neurotoxicity and reproductive disruptions were validated via multilevel toxicological endpoints. Specifically, locomotor behavioral changes proved the potency of neurotoxicity, which may be caused by disturbance of muscular proteins and calcium homeostasis; decreases of sex hormone levels and transcriptional changes of genes related to the hypothalamic-pituitary-gonad-liver axis confirmed reproductive disruptions upon DBDPE exposure. In summary, our results suggested that DBDPE primarily accumulated in the brain and evoked neurotoxicity and reproductive disruptions in female zebrafish. These findings can provide important clues for a further mechanism study and risk assessment of DBDPE.

Proteogenomic Analysis Provides Novel Insight into Genome Annotation and Nitrogen Metabolism in Nostoc sp. PCC 7120

Cyanobacteria, capable of oxygenic photosynthesis, play a vital role in nitrogen and carbon cycles. Nostoc sp. PCC 7120 (Nostoc 7120) is a model cyanobacterium commonly used to study cell differentiation and nitrogen metabolism. Although its genome was released in 2002, a high-quality genome annotation remains unavailable for this model cyanobacterium. Therefore, in this study, we performed an in-depth proteogenomic analysis based on high-resolution mass spectrometry (MS) data to refine the genome annotation of Nostoc 7120. We unambiguously identified 5,519 predicted protein-coding genes and revealed 26 novel genes, 75 revised genes, and 27 different kinds of posttranslational modifications in Nostoc 7120. A subset of these novel proteins were further validated at both the mRNA and peptide levels. Functional analysis suggested that many newly annotated proteins may participate in nitrogen or cadmium/mercury metabolism in Nostoc 7120. Moreover, we constructed an updated Nostoc 7120 database based on our proteogenomic results and presented examples of how the updated database could be used to improve the annotation of proteomic data. Our study provides the most comprehensive annotation of the Nostoc 7120 genome thus far and will serve as a valuable resource for the study of nitrogen metabolism in Nostoc 7120.

IMPORTANCE Cyanobacteria are a large group of prokaryotes capable of oxygenic photosynthesis and play a vital role in nitrogen and carbon cycles on Earth. Nostoc 7120 is a commonly used model cyanobacterium for studying cell differentiation and nitrogen metabolism. In this study, we presented the first comprehensive draft map of the Nostoc 7120 proteome and a wide range of posttranslational modifications. In addition, we constructed an updated database of Nostoc 7120 based on our proteogenomic results and presented examples of how the updated database could be used for system-level studies of Nostoc 7120. Our study provides the most comprehensive annotation of Nostoc 7120 genome and a valuable resource for the study of nitrogen metabolism in this model cyanobacterium.

Quantitative Proteomics Reveals the Protein Regulatory Network of Anabaena sp. PCC 7120 under Nitrogen Deficiency

Anabaena sp. PCC 7120 (Anabaena 7120) is a photoautotrophic filamentous cyanobacterium capable of fixing atmospheric nitrogen. It is a model organism used for studying cell differentiation and nitrogen fixation. Under nitrogen deficiency, Anabaena 7120 forms specialized heterocysts capable of nitrogen fixation. However, the molecular mechanisms involved in the cyanobacterial adaptation to nitrogen deficiency are not well understood. Here, we employed a label-free quantitative proteomic strategy to systematically investigate the nitrogen deficiency response of Anabaena 7120 at different time points. In total, 363, 603, and 669 proteins showed significant changes in protein abundance under nitrogen deficiency for 3, 12, and 24 h, respectively. With mapping onto metabolic pathways, we revealed proteomic perturbation and regulation of carbon and nitrogen metabolism in response to nitrogen deficiency. Functional analysis confirmed the involvement of nitrogen stress-responsive proteins in biological processes, including nitrogen fixation, photosynthesis, energy and carbon metabolism, and heterocyst development. The expression of 10 proteins at different time points was further validated by using multiple reaction monitoring assays. In particular, many dysregulated proteins were found to be time-specific and involved in heterocyst development, providing new candidates for future functional studies in this model cyanobacterium. These results provide novel insights into the molecular mechanisms of nitrogen stress responses and heterocyst development in Anabaena 7120.

Comprehensive and Functional Analysis of Horizontal Gene Transfer Events in Diatoms

Diatoms are a diverse group of mainly photosynthetic algae, responsible for 20% of worldwide oxygen production, which can rapidly respond to favorable conditions and often outcompete other phytoplankton. We investigated the contribution of horizontal gene transfer (HGT) to its ecological success. A large-scale phylogeny-based prokaryotic HGT detection procedure across nine sequenced diatoms showed that 3-5% of their proteome has a horizontal origin and a large influx occurred at the ancestor of diatoms. More than 90% of HGT genes are expressed, and species-specific HGT genes in Phaeodactylum tricornutum undergo strong purifying selection. Genes derived from HGT are implicated in several processes including environmental sensing and expand the metabolic toolbox. Cobalamin (vitamin B12) is an essential cofactor for roughly half of the diatoms and is only produced by bacteria. Five consecutive genes involved in the final synthesis of the cobalamin biosynthetic pathway, which could function as scavenging and repair genes, were detected as HGT. The full suite of these genes was detected in the cold-adapted diatom Fragilariopsis cylindrus. This might give diatoms originating from the Southern Ocean, a region typically depleted in cobalamin, a competitive advantage. Overall, we show that HGT is a prevalent mechanism that is actively used in diatoms to expand its adaptive capabilities.

The role of micropeptides in biology

Micropeptides are small polypeptides coded by small open-reading frames. Progress in computational biology and the analyses of large-scale transcriptomes and proteomes have revealed that mammalian genomes produce a large number of transcripts encoding micropeptides. Many of these have been previously annotated as long noncoding RNAs. The role of micropeptides in cellular homeostasis maintenance has been demonstrated. This review discusses different types of micropeptides as well as methods to identify them, such as computational approaches, ribosome profiling, and mass spectrometry.

Genome-wide analysis of allele-specific expression of genes in the model diatom Phaeodactylum tricornutum

Recent advances in next generation sequencing technologies have allowed the discovery of widespread autosomal allele-specific expression (aASE) in mammals and plants with potential phenotypic effects. Extensive numbers of genes with allele-specific expression have been described in the diatom Fragilariopsis cylindrus in association with adaptation to external cues, as well as in Fistulifera solaris in the context of natural hybridization. However, the role of aASE and its extent in diatoms remain elusive. In this study, we investigate allele-specific expression in the model diatom Phaeodactylum tricornutum by the re-analysis of previously published whole genome RNA sequencing data and polymorphism calling. We found that 22% of P. tricornutum genes show moderate bias in allelic expression while 1% show nearly complete monoallelic expression. Biallelic expression associates with genes encoding components of protein metabolism while moderately biased genes associate with functions in catabolism and protein transport. We validated candidate genes by pyrosequencing and found that moderate biases in allelic expression were less stable than monoallelically expressed genes that showed consistent bias upon experimental validations at the population level and in subcloning experiments. Our approach provides the basis for the analysis of aASE in P. tricornutum and could be routinely implemented to test for variations in allele expression under different environmental conditions.

A novel phosphoinositide kinase Fab1 regulates biosynthesis of pathogenic aflatoxin in Aspergillus flavus

Aspergillus flavus (A. flavus) is one of the most important model environmental fungi which can produce a potent toxin and carcinogen known as aflatoxin. Aflatoxin contamination causes massive agricultural economic loss and a critical human health issue each year. Although a functional vacuole has been highlighted for its fundamental importance in fungal virulence, the molecular mechanisms of the vacuole in regulating the virulence of A. flavus remain largely unknown. Here, we identified a novel vacuole-related protein in A. flavus, the ortholog of phosphatidylinositol-3-phosphate-5-kinase (Fab1) in Saccharomyces cerevisiae. This kinase was located at the vacuolar membrane, and loss of fab1 function was found to affect the growth, conidia and sclerotial development, cellular acidification and metal ion homeostasis, aflatoxin production and pathogenicity of A. flavus. Further functional analysis revealed that Fab1 was required to maintain the vacuole size and cell morphology. Additional quantitative proteomic analysis suggested that Fab1 was likely to play an important role in maintaining vacuolar/cellular homeostasis, with vacuolar dysregulation upon fab1 deletion leading to impaired aflatoxin synthesis in this fungus. Together, these results provide insight into the molecular mechanisms by which this pathogen produces aflatoxin and mediates its pathogenicity, and may facilitate dissection of the vacuole-mediated regulatory network in A. flavus.

Proteogenomic Characterization of the Pathogenic Fungus Aspergillus flavus Reveals Novel Genes Involved in Aflatoxin Production

Aspergillus flavus (A. flavus), a pathogenic fungus, can produce carcinogenic and toxic aflatoxins that are a serious agricultural and medical threat worldwide. Attempts to decipher the aflatoxin biosynthetic pathway have been hampered by the lack of a high-quality genome annotation for A. flavus. To address this gap, we performed a comprehensive proteogenomic analysis using high-accuracy mass spectrometry data for this pathogen. The resulting high-quality data set confirmed the translation of 8724 previously predicted genes and identified 732 novel proteins, 269 splice variants, 447 single amino acid variants, 188 revised genes. A subset of novel proteins was experimentally validated by RT-PCR and synthetic peptides. Further functional annotation suggested that a number of the identified novel proteins may play roles in aflatoxin biosynthesis and stress responses in A. flavus. This comprehensive strategy also identified a wide range of posttranslational modifications (PTMs), including 3461 modification sites from 1765 proteins. Functional analysis suggested the involvement of these modified proteins in the regulation of cellular metabolic and aflatoxin biosynthetic pathways. Together, we provided a high-quality annotation of A. flavus genome and revealed novel insights into the mechanisms of aflatoxin production and pathogenicity in this pathogen.

Large-Scale Discovery of Non-conventional Peptides in Maize and Arabidopsis through an Integrated Peptidogenomic Pipeline

Non-conventional peptides (NCPs), which include small open reading frame-encoded peptides, play critical roles in fundamental biological processes. In this study, we developed an integrated peptidogenomic pipeline using high-throughput mass spectra to probe a customized six-frame translation database and applied it to large-scale identification of NCPs in plants.A total of 1993 and 1860 NCPs were unambiguously identified in maize and Arabidopsis, respectively. These NCPs showed distinct characteristics compared with conventional peptides and were derived from introns, 3' UTRs, 5' UTRs, junctions, and intergenic regions. Furthermore, our results showed that translation events in unannotated transcripts occur more broadly than previously thought. In addition, we found that dozens of maize NCPs are enriched within regions associated with phenotypic variations and domestication selection, indicating that they potentially are involved in genetic regulation of complex traits and domestication in maize. Taken together, our study developed an integrated peptidogenomic pipeline for large-scale identification of NCPs in plants, which would facilitate global characterization of NCPs from other plants. The identification of large-scale NCPs in both monocot (maize) and dicot (Arabidopsis) plants indicates that a large portion of plant genome can be translated into biologically functional molecules, which has important implications for functional genomic studies.

Proteome-Wide Identification of Lysine Propionylation in the Conidial and Mycelial Stages of Trichophyton rubrum

Posttranslational modifications (PTMs) exist in a wide variety of organisms and play key roles in regulating various essential biological processes. Lysine propionylation is a newly discovered PTM that has rarely been identified in fungi. Trichophyton rubrum (T. rubrum) is one of the most common fungal pathogens in the world and has been studied as an important model organism of anthropic pathogenic filamentous fungi. In this study, we performed a proteome-wide propionylation analysis in the conidial and mycelial stages of T. rubrum. A total of 157 propionylated sites on 115 proteins were identified, and the high confidence of propionylation identification was validated by parallel reaction monitoring (PRM) assay. The results show that the propionylated proteins were mostly involved in various metabolic pathways. Histones and 15 pathogenicity-related proteins were also targets for propionylation modification, suggesting their roles in epigenetic regulation and pathogenicity. A comparison of the conidial and mycelial stages revealed that most propionylated proteins and sites were growth-stage specific and independent of protein abundance. Based on the function classifications, the propionylated proteins had a similar distribution in both stages; however, some differences were also identified. Furthermore, our results show that the concentration of propionyl-CoA had a significant influence on the propionylation level. In addition to the acetylation, succinylation and propionylation identified in T. rubrum, 26 other PTMs were also found to exist in this fungus. Overall, our study provides the first global propionylation profile of a pathogenic fungus. These results would be a foundation for further research on the regulation mechanism of propionylation in T. rubrum, which will enhance our understanding of the physiological features of T. rubrum and provide some clues for the exploration of improved therapies to treat this medically important fungus.

Identification, characterization and expression analysis of lineage-specific genes within Triticeae

Lineage-specific genes (LSGs) are a set of genes in a given taxon without significant sequence similarity to genes and intergenic sequences of other taxa and are functional. The tribe Triticeae mainly includes species of different ploidy levels, such as staple food crops wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.). This study is aimed at mining and characterizing the Triticeae-specific genes (TSGs) using expressed sequence data of wheat. A total of 3812 TSGs was identified and they were generally characterized by smaller size, fewer exons, shorter open reading frames and lower expression levels. Most TSGs were expressed with tissue preference and many of them were predominantly expressed in reproduction related tissues, especially in young stamen. Nearly one third of the TSGs were stress-responsive and inducible under abiotic and/or biotic stresses. A co-expression-based annotation supported the relevance of some TSGs with reproduction and stress responses, indicating their potential economic importance.

Acute toxicity of the fungicide azoxystrobin on the diatom Phaeodactylum tricornutum

Azoxystrobin (AZ) is an effective broad-spectrum fungicide. Due to its extensive application, AZ is detectable in aquatic ecosystems and thus influences aquatic organisms. In this study, the acute toxicity (96 h) of AZ at concentrations of 1.0 mg/L and 5.0 mg/L on the diatom Phaeodactylum tricornutum were examined. At the tested concentrations, AZ significantly inhibited P. tricornutum growth and destroyed its cellular structure. Furthermore, the mechanisms of AZ-induced toxicity on P. tricornutum changed as the exposure time extended. Forty-eight hours after exposure, AZ inhibited P. tricornutum growth primarily via inducing oxidative stress, which increased the activity of two main antioxidant enzymes, superoxide dismutase and peroxidase, and inhibited energy metabolism. However, after 96 h of treatment, the decline in the photosynthetic capacity of P. tricornutum demonstrated that the photosystem was the main AZ target. The pigment content and expression levels of genes related to photosynthetic electron transfer reactions were also significantly decreased. The present study describes AZ toxicity in P. tricornutum and is very valuable for assessing the environmental risk of AZ.