Sequence, structure and evolutionary analysis of cold shock domain proteins, a member of OB fold family

The genome-wide characterisation of cold shock proteins and prominent roles involved in cold response by configuring metabolic pathways in Haemaphysalis longicornis

Cold shock proteins are relatively conserved in evolution and are involved in regulating various life activities, including cell proliferation, nutritional stress and cold adaptation. However, information about the function and regulation of cold shock proteins in ticks during cold response remains meagre. In the present study, six cold shock protein genes were identified from the important vector tick Haemaphysalis longicornis, which were named as HlY-box1, HlY-box2, HlY-box3, HlY-box4, HlY-box5 and HlY-box6. Spatiotemporal expression dynamics revealed dynamic expressions varied significantly after low-temperature treatment, with different expression patterns observed over prolonged exposure periods. Then the function and regulation of cold shock protein genes during the cold response of H. longicornis were explored. RNA interference (RNAi) efficiently knocked down these genes, significantly increasing tick mortality under cold stress. Transcriptomic analysis following HlY-box4 knockdown identified 336 differentially expressed genes (DEGs), which were mainly annotated in the MAPK signalling pathway and metabolism pathway. Proteomic analysis identified 632 differentially expressed proteins associated with ATP-dependent chromatin remodelling, metabolic pathway, spliceosome, ribosome and nucleoplasmic transport pathways. The results highlight the critical roles of cold shock proteins (CSPs) in tick cold responses, primarily through regulating metabolic pathways, and provide a foundation for further exploration of their molecular mechanisms.

Rho-dependent termination: a bacterial evolutionary capacitor for stress resistance

Since the Modern Synthesis, interest has grown in resolving the "black box" between genotype and phenotype. Contained within this black box are highly plastic RNA and proteins with global effects on chromosome integrity and gene expression that serve as evolutionary capacitors - elements that enable the accumulation and buffering of genetic variation in normal conditions and reveal hidden genetic variation when induced by environmental stress. Discussion of evolutionary capacitors has primarily focused on eukaryotic translation factors and chaperones, such as Hsp90 and PSI+ prion. However, due to the coupling of transcription and translation in prokaryotes, transcription factors can be equally impactful in the modulation of gene expression and phenotypes. In this review, we discuss the prokaryotic transcription terminator Rho and how mutagenesis and plasticity of Rho influence epistasis, evolvability, and adaptation to stress in bacteria. We discuss the effects of variation in Rho generated by nature, laboratory mutagenesis, and experimental evolution; and how this variation is constrained or encouraged by Rho's extensive network of protein interactors. Exploring Rho's role as an evolutionary capacitor, along with identifying additional elements that can serve this function, can significantly advance our understanding of how organisms adapt to thrive in diverse environments.

From genes to traits: Trends in RNA-binding proteins and their role in plant trait development: A review

RNA-binding proteins (RBPs) are essential for cellular functions by attaching to RNAs, creating dynamic ribonucleoprotein complexes (RNPs) essential for managing RNA throughout its life cycle. These proteins are critical to all post-transcriptional processes, impacting vital cellular functions during development and adaptation to environmental changes. Notably, in plants, RBPs are critical for adjusting to inconsistent environmental conditions, with recent studies revealing that plants possess, more prominent, and both novel and conserved RBP families compared to other eukaryotes. This comprehensive review delves into the varied RBPs covering their structural attributes, domain base function, and their interactions with RNA in metabolism, spotlighting their role in regulating post-transcription and splicing and their reaction to internal and external stimuli. It highlights the complex regulatory roles of RBPs, focusing on plant trait regulation and the unique functions they facilitate, establishing a foundation for appreciating RBPs' significance in plant growth and environmental response strategies.

C. elegans LIN-66 mediates EIF-3/eIF3-dependent protein translation via a cold-shock domain

Protein translation initiation is a conserved process involving many proteins acting in concert. The 13 subunit eukaryotic initiation factor 3 (eIF3) complex is essential for assembly of the pre-initiation complex that scans mRNA and positions ribosome at the initiation codon. We previously reported that a gain-of-function (gf) mutation affecting the G subunit of the Caenorhabditis elegans eIF3 complex, eif-3.g(gf), selectively modulates protein translation in the ventral cord cholinergic motor neurons. Here, through unbiased genetic suppressor screening, we identified that the gene lin-66 mediates eif-3.g(gf)-dependent protein translation in motor neurons. LIN-66 is composed largely of low-complexity amino acid sequences with unknown functional domains. We combined bioinformatics analysis with in vivo functional dissection and identified a cold-shock domain in LIN-66 critical for its function. In cholinergic motor neurons, LIN-66 shows a close association with EIF-3.G in the cytoplasm. The low-complexity amino acid sequences of LIN-66 modulate its subcellular pattern. As cold-shock domains function broadly in RNA regulation, we propose that LIN-66 mediates stimulus-dependent protein translation by facilitating the interaction of mRNAs with EIF-3.G.

CoCoNuTs are a diverse subclass of Type IV restriction systems predicted to target RNA

A comprehensive census of McrBC systems, among the most common forms of prokaryotic Type IV restriction systems, followed by phylogenetic analysis, reveals their enormous abundance in diverse prokaryotes and a plethora of genomic associations. We focus on a previously uncharacterized branch, which we denote coiled-coil nuclease tandems (CoCoNuTs) for their salient features: the presence of extensive coiled-coil structures and tandem nucleases. The CoCoNuTs alone show extraordinary variety, with three distinct types and multiple subtypes. All CoCoNuTs contain domains predicted to interact with translation system components, such as OB-folds resembling the SmpB protein that binds bacterial transfer-messenger RNA (tmRNA), YTH-like domains that might recognize methylated tmRNA, tRNA, or rRNA, and RNA-binding Hsp70 chaperone homologs, along with RNases, such as HEPN domains, all suggesting that the CoCoNuTs target RNA. Many CoCoNuTs might additionally target DNA, via McrC nuclease homologs. Additional restriction systems, such as Type I RM, BREX, and Druantia Type III, are frequently encoded in the same predicted superoperons. In many of these superoperons, CoCoNuTs are likely regulated by cyclic nucleotides, possibly, RNA fragments with cyclic termini, that bind associated CARF (CRISPR-Associated Rossmann Fold) domains. We hypothesize that the CoCoNuTs, together with the ancillary restriction factors, employ an echeloned defense strategy analogous to that of Type III CRISPR-Cas systems, in which an immune response eliminating virus DNA and/or RNA is launched first, but then, if it fails, an abortive infection response leading to PCD/dormancy via host RNA cleavage takes over.

Variation in base composition, structure-function relationships, and origins of structural repetition in bacterial rpsA gene

Protein domain repeats are known to arise due to tandem duplications of internal genes. However, the understanding of the underlying mechanisms of this process is incomplete. The goal of this work was to investigate the mechanism of occurrence of repeat expansion based on studying the sequences of 1324 rpsA genes of bacterial S1 ribosomal proteins containing different numbers of S1 structural domains. The rpsA gene encodes ribosomal S1 protein, which is essential for cell viability as it interacts with both mRNA and proteins. Gene ontology (GO) analysis of S1 domains in ribosomal S1 proteins revealed that bacterial protein sequences in S1 mainly have 3 types of molecular functions: RNA binding activity, nucleic acid activity, and ribosome structural component. Our results show that the maximum value of rpsA gene identity for full-length proteins was found for S1 proteins containing six structural domains (58%). Analysis of consensus sequences showed that parts of the rpsA gene encoding separate S1 domains have no a strictly repetitive structure between groups containing different numbers of S1 domains. At the same time, gene regions encoding some conserved residues that form the RNA-binding site remain conserved. The detected phylogenetic similarity suggests that the proposed fold of the rpsA translation initiation region of Escherichia coli has functional value and is important for translational control of rpsA gene expression in other bacterial phyla, but not only in gamma Proteobacteria.

CoCoNuTs: A diverse subclass of Type IV restriction systems predicted to target RNA

A comprehensive census of McrBC systems, among the most common forms of prokaryotic Type IV restriction systems, followed by phylogenetic analysis, reveals their enormous abundance in diverse prokaryotes and a plethora of genomic associations. We focus on a previously uncharacterized branch, which we denote CoCoNuTs (coiled-coil nuclease tandems) for their salient features: the presence of extensive coiled-coil structures and tandem nucleases. The CoCoNuTs alone show extraordinary variety, with 3 distinct types and multiple subtypes. All CoCoNuTs contain domains predicted to interact with translation system components, such as OB-folds resembling the SmpB protein that binds bacterial transfer-messenger RNA (tmRNA), YTH-like domains that might recognize methylated tmRNA, tRNA, or rRNA, and RNA-binding Hsp70 chaperone homologs, along with RNases, such as HEPN domains, all suggesting that the CoCoNuTs target RNA. Many CoCoNuTs might additionally target DNA, via McrC nuclease homologs. Additional restriction systems, such as Type I RM, BREX, and Druantia Type III, are frequently encoded in the same predicted superoperons. In many of these superoperons, CoCoNuTs are likely regulated by cyclic nucleotides, possibly, RNA fragments with cyclic termini, that bind associated CARF (CRISPR-Associated Rossmann Fold) domains. We hypothesize that the CoCoNuTs, together with the ancillary restriction factors, employ an echeloned defense strategy analogous to that of Type III CRISPR-Cas systems, in which an immune response eliminating virus DNA and/or RNA is launched first, but then, if it fails, an abortive infection response leading to PCD/dormancy via host RNA cleavage takes over.

The Glycine-Rich RNA-Binding Protein Is a Vital Post-Transcriptional Regulator in Crops

Glycine-rich RNA binding proteins (GR-RBPs), a branch of RNA binding proteins (RBPs), play integral roles in regulating various aspects of RNA metabolism regulation, such as RNA processing, transport, localization, translation, and stability, and ultimately regulate gene expression and cell fate. However, our current understanding of GR-RBPs has predominantly been centered on Arabidopsis thaliana, a model plant for investigating plant growth and development. Nonetheless, an increasing body of literature has emerged in recent years, shedding light on the presence and functions of GRPs in diverse crop species. In this review, we not only delineate the distinctive structural domains of plant GR-RBPs but also elucidate several contemporary mechanisms of GR-RBPs in the post-transcriptional regulation of RNA. These mechanisms encompass intricate processes, including RNA alternative splicing, polyadenylation, miRNA biogenesis, phase separation, and RNA translation. Furthermore, we offer an exhaustive synthesis of the diverse roles that GR-RBPs fulfill within crop plants. Our overarching objective is to provide researchers and practitioners in the field of agricultural genetics with valuable insights that may inform and guide the application of plant genetic engineering for enhanced crop development and sustainable agriculture.

Multiple domains of the integral KREPA3 protein are critical for the structure and precise functions of RNA editing catalytic complexes in Trypanosoma brucei

The gRNA directed U-insertion and deletion editing of mitochondrial mRNAs that is essential in different life-cycle stages for the protozoan parasite Trypanosoma brucei is performed by three similar multiprotein catalytic complexes (CCs) that contain the requisite enzymes. These CCs also contain a common set of eight proteins that have no apparent direct catalytic function, including six that have an OB-fold domain. We show here that one of these OB-fold proteins, KREPA3 (A3), has structural homology to other editing proteins, is essential for editing, and is multifunctional. We investigated A3 function by analyzing the effects of single amino acid loss of function mutations, most of which were identified by screening bloodstream form (BF) parasites for loss of growth following random mutagenesis. Mutations in the zinc fingers (ZFs), an intrinsically disordered region (IDR), and several within or near the carboxy-terminal OB-fold domain variably impacted CC structural integrity and editing. Some mutations resulted in almost complete loss of CCs and its proteins and editing, whereas others retained CCs but had aberrant editing. All but a mutation which is near the OB-fold affected growth and editing in BF but not procyclic form (PF) parasites. These data indicate that multiple positions within A3 have essential functions that contribute to the structural integrity of CCs, the precision of editing and the developmental differences in editing between BF and PF stages.

Multiple domains of the integral KREPA3 protein are critical for the structure and precise functions of RNA Editing Catalytic Complexes in Trypanosoma brucei

The gRNA directed U-insertion and deletion editing of mitochondrial mRNAs that is essential in different life cycle stages for the protozoan parasite Trypanosoma brucei is performed by three similar multi-protein catalytic complexes (CCs) that contain the requisite enzymes. These CCs also contain a common set of eight proteins that have no apparent direct catalytic function, including six that have an OB-fold domain. We show here that one of these OB-fold proteins, KREPA3 (A3), has structural homology to other editing proteins, is essential for editing and is multifunctional. We investigated A3 function by analyzing the effects of single amino acid loss of function mutations most of which were identified by screening bloodstream form (BF) parasites for loss of growth following random mutagenesis. Mutations in the ZFs, an intrinsically disordered region (IDR) and several within or near the C-terminal OB-fold domain variably impacted CC structural integrity and editing. Some mutations resulted in almost complete loss of CCs and its proteins and editing whereas others retained CCs but had aberrant editing. All but a mutation which is near the OB-fold affected growth and editing in BF but not procyclic form (PF) parasites. These data indicate that multiple positions within A3 have essential functions that contribute to the structural integrity of CCs, the precision of editing and the developmental differences in editing between BF and PF stages.

DgCspC gene overexpression improves cotton yield and tolerance to drought and salt stress comparison with wild-type plants

Drought and high salinity are key limiting factors for cotton quality and yield. Therefore, research is increasingly focused on mining effective genes to improve the stress resistance of cotton. Few studies have demonstrated that bacterial Cold shock proteins (Csps) overexpression can enhance plants stress tolerance. Here, we first identified and cloned a gene DgCspC encoding 88 amino acids (aa) with an open reading frame (ORF) of 264 base pairs (bp) from a Deinococcus gobiensis I-0 with high resistance to strong radiation, drought, and high temperature. In this study, heterologous expression of DgCspC promoted cotton growth, as exhibited by larger leaf size and higher plant height than the wild-type plants. Moreover, transgenic cotton lines showed higher tolerance to drought and salts stresses than wild-type plants, as revealed by susceptibility phenotype and physiological indexes. Furthermore, the enhanced stresses tolerance was attributed to high capacity of cellular osmotic regulation and ROS scavenging resulted from DgCspC expression modulating relative genes upregulated to cause proline and betaine accumulation. Meanwhile, photosynthetic efficiency and yield were significantly higher in the transgenic cotton than in the wild-type control under field conditions. This study provides a newly effective gene resource to cultivate new cotton varieties with high stresses resistance and yield.

Impact of Single Amino Acid Substitutions in Parkinsonism-Associated Deglycase-PARK7 and Their Association with Parkinson's Disease

Parkinsonism-associated deglycase-PARK7/DJ-1 (PARK7) is a multifunctional protein having significant roles in inflammatory and immune disorders and cell protection against oxidative stress. Mutations in PARK7 may result in the onset and progression of a few neurodegenerative disorders such as Parkinson's disease. This study has analyzed the non-synonymous single nucleotide polymorphisms (nsSNPs) resulting in single amino acid substitutions in PARK7 to explore its disease-causing variants and their structural dysfunctions. Initially, we retrieved the mutational dataset of PARK7 from the Ensembl database and performed detailed analyses using sequence-based and structure-based approaches. The pathogenicity of the PARK7 was then performed to distinguish the destabilizing/deleterious variants. Aggregation propensity, noncovalent interactions, packing density, and solvent accessible surface area analyses were carried out on the selected pathogenic mutations. The SODA study suggested that mutations in PARK7 result in aggregation, inducing disordered helix and altering the strand propensity. The effect of mutations alters the number of hydrogen bonds and hydrophobic interactions in PARK7, as calculated from the Arpeggio server. The study indicated that the alteration in the hydrophobic contacts and frustration of the protein could alter the stability of the missense variants of the PARK7, which might result in disease progression. This study provides a detailed understanding of the destabilizing effects of single amino acid substitutions in PARK7.

Structure and mechanism of the RNA dependent RNase Cas13a from Rhodobacter capsulatus

Cas13a are single-molecule effectors of the Class II, Type VI family of CRISPR-Cas systems that are part of the bacterial and archaeal defense systems. These RNA-guided and RNA-activated RNA endonucleases are characterized by their ability to cleave target RNAs complementary to the crRNA-spacer sequence, as well as bystander RNAs in a sequence-unspecific manner. Due to cleavage of cellular transcripts they induce dormancy in the host cell and thus protect the bacterial population by aborting the infectious cycle of RNA-phages. Here we report the structural and functional characterization of a Cas13a enzyme from the photo-auxotrophic purple bacteria Rhodobacter capsulatus. The X-ray crystal structure of the RcCas13a-crRNA complex reveals its distinct crRNA recognition mode as well as the enzyme in its contracted, pre-activation conformation. Using site-directed mutagenesis in combination with mass spectrometry, we identified key residues responsible for pre-crRNA processing by RcCas13a in its distinct catalytic site, and elucidated the acid-base mediated cleavage reaction mechanism. In addition, RcCas13a cleaves target-RNA as well as bystander-RNAs in Escherichia coli which requires its catalytic active HEPN (higher eukaryotes and prokaryotes nucleotide binding) domain nuclease activity. Our data provide further insights into the molecular mechanisms and function of this intriguing family of RNA-dependent RNA endonucleases that are already employed as efficient tools for RNA detection and regulation of gene expression.

The structure of the Cas13a RNase from the purple bacterium R. capsulatus in complex with its crRNA is reported here. The study reveals that the enzyme combines shape and sequence-specific readout to recognize its crRNA.

Characteristic Features of Protein Interaction with Single- and Double-Stranded RNA

The review discusses differences between the specific protein interactions with single- and double-stranded RNA molecules using the data on the structure of RNA-protein complexes. Proteins interacting with the single-stranded RNAs form contacts with RNA bases, which ensures recognition of specific nucleotide sequences. Formation of such contacts with the double-stranded RNAs is hindered, so that the proteins recognize unique conformations of the RNA spatial structure and interact mainly with the RNA sugar-phosphate backbone.

In Silico Structural and Functional Analysis of Cold Shock Proteins in Pseudomonas fluorescens PF08 from Marine Fish

ABSTRACT

Pseudomonas fluorescens is a specific spoilage microorganism of refrigerated marine fish, and is highly adapted to low temperature. Cold shock proteins (CSPs) play an important role in cold adaptation of bacteria. In this study, CSP genes were identified from the genome of P. fluorescens PF08 by search of the conserved domain of CSPs with HMMER software, and the CSP physicochemical properties, structures, and functions were analyzed through bioinformatics. Five typical CSPs were identified in the P. fluorescens PF08 genome (PfCSPs). All five PfCSPs are small hydrophilic acidic proteins with a molecular mass of ca. 7.4 kDa. They are located in the cytoplasm and are nonsecretory and nontransmembrane proteins. Multiple sequence alignment analysis indicated that the CSPs are highly conserved between species, especially in DNA-binding sites and RNA-binding motifs that can bind to single-stranded DNA and RNA. The five PfCSPs clustered with CspD from Escherichia coli and Salmonella Typhimurium, which suggests a close homology and high functional similarity among the five PfCSPs and CspD. The secondary and tertiary structures of the PfCSPs are in accordance with the characteristics of the CSP family, and ligand binding sites with higher likelihood were found in PfCSPs. The five PfCSPs were predicted to interact with some of the same proteins that are involved in virulence, stress responses (including to low temperature), cell growth, ribosome assembly, and RNA degradation. The results provide further elucidation of the function of CSPs in adaptation to low temperatures by P. fluorescens.

HIGHLIGHTS

Identification of Amyloidogenic Regions in Pseudomonas aeruginosa Ribosomal S1 Protein

Bacterial S1 protein is a functionally important ribosomal protein. It is a part of the 30S ribosomal subunit and is also able to interact with mRNA and tmRNA. An important feature of the S1 protein family is a strong tendency towards aggregation. To study the amyloidogenic properties of S1, we isolated and purified the recombinant ribosomal S1 protein of Pseudomonas aeruginosa. Using the FoldAmyloid, Waltz, Pasta 2.0, and AGGRESCAN programs, amyloidogenic regions of the protein were predicted, which play a key role in its aggregation. The method of limited proteolysis in combination with high performance liquid chromatography and mass spectrometric analysis of the products, made it possible to identify regions of the S1 protein from P. aeruginosa that are protected from the action of proteinase K, trypsin, and chymotrypsin. Sequences of theoretically predicted and experimentally identified amyloidogenic regions were used to synthesize four peptides, three of which demonstrated the ability to form amyloid-like fibrils, as shown by electron microscopy and fluorescence spectroscopy. The identified amyloidogenic sites can further serve as a basis for the development of new antibacterial peptides against the pathogenic microorganism P. aeruginosa.

Structural genomics approach to investigate deleterious impact of nsSNPs in conserved telomere maintenance component 1

Conserved telomere maintenance component 1 (CTC1) is an important component of the CST (CTC1-STN1-TEN1) complex, involved in maintaining the stability of telomeric DNA. Several non-synonymous single-nucleotide polymorphisms (nsSNPs) in CTC1 have been reported to cause Coats plus syndrome and Dyskeratosis congenital diseases. Here, we have performed sequence and structure analyses of nsSNPs of CTC1 using state-of-the-art computational methods. The structure-based study focuses on the C-terminal OB-fold region of CTC1. There are 11 pathogenic mutations identified, and detailed structural analyses were performed. These mutations cause a significant disruption of noncovalent interactions, which may be a possible reason for CTC1 instability and consequent diseases. To see the impact of such mutations on the protein conformation, all-atom molecular dynamics (MD) simulations of CTC1-wild-type (WT) and two of the selected mutations, R806C and R806L for 200 ns, were carried out. A significant conformational change in the structure of the R806C mutant was observed. This study provides a valuable direction to understand the molecular basis of CTC1 dysfunction in disease progression, including Coats plus syndrome.

Cold-Shock Domains-Abundance, Structure, Properties, and Nucleic-Acid Binding

Simple Summary

Proteins are composed of compact domains, often of known three-dimensional structure, and natively unstructured polypeptide regions. The abundant cold-shock domain is among the set of canonical nucleic acid-binding domains and conserved from bacteria to man. Proteins containing cold-shock domains serve a large variety of biological functions, which are mostly linked to DNA or RNA binding. These functions include the regulation of transcription, RNA splicing, translation, stability and sequestration. Cold-shock domains have a simple architecture with a conserved surface ideally suited to bind single-stranded nucleic acids. Because the binding is mostly by non-specific molecular interactions which do not involve the sugar-phosphate backbone, cold-shock domains are not strictly sequence-specific and do not discriminate reliably between DNA and RNA. Many, but not all functions of cold shock-domain proteins in health and disease can be understood based of the physical and structural properties of their cold-shock domains.

Abstract

The cold-shock domain has a deceptively simple architecture but supports a complex biology. It is conserved from bacteria to man and has representatives in all kingdoms of life. Bacterial cold-shock proteins consist of a single cold-shock domain and some, but not all are induced by cold shock. Cold-shock domains in human proteins are often associated with natively unfolded protein segments and more rarely with other folded domains. Cold-shock proteins and domains share a five-stranded all-antiparallel β-barrel structure and a conserved surface that binds single-stranded nucleic acids, predominantly by stacking interactions between nucleobases and aromatic protein sidechains. This conserved binding mode explains the cold-shock domains’ ability to associate with both DNA and RNA strands and their limited sequence selectivity. The promiscuous DNA and RNA binding provides a rationale for the ability of cold-shock domain-containing proteins to function in transcription regulation and DNA-damage repair as well as in regulating splicing, translation, mRNA stability and RNA sequestration.

A Systems View of the Genome Guardians: Mapping the Signaling Circuitry Underlying Oligonucleotide/Oligosaccharide-Binding Fold Proteins

The oligonucleotide/oligosaccharide-binding (OB)-fold domain proteins are considered as genome guardians, whose functions are extending beyond genomic stability. The broad functional diversity of the OB-fold proteins is attributed to their protein-DNA, protein-RNA, and protein-protein interactions (PPI). To understand the connectivity of the human OB-fold proteins, we report here a systems-level approach. Specifically, we mapped all human OB-fold PPI networks and evaluated topological features such as network robustness and network hub, among others. We found that the OB-fold network comprised of 227 nodes forming 5523 interactions, and has a scale-free topology having UBA52, ATR, and TP53 as leading hub proteins that control efficient communication within the network. Furthermore, four different clusters and subclusters have been identified, which are implicated in diverse cellular processes, including DNA replication, repair, maintenance of genomic stability, RNA processing, spermatogenesis, complement system, and telomere maintenance. The importance of these clusters is further strengthened by knockout studies, which showed a significant decrease in topological properties. In summary, this study provides new insights on the role of OB-fold protein as genome guardians in regard to the underlying mechanism of signaling pathways, the roles of key regulators, and thus, offers new prospects as potential targets for diagnostics and therapeutics purposes.

Domain-centric database to uncover structure of minimally characterized viral genomes

Protein domain-based approaches to analyzing sequence data are valuable tools for examining and exploring genomic architecture across genomes of different organisms. Here, we present a complete dataset of domains from the publicly available sequence data of 9,051 reference viral genomes. The data provided contain information such as sequence position and neighboring domains from 30,947 pHMM-identified domains from each reference viral genome. Domains were identified from viral whole-genome sequence using automated profile Hidden Markov Models (pHMM). This study also describes the framework for constructing "domain neighborhoods", as well as the dataset representing it. These data can be used to examine shared and differing domain architectures across viral genomes, to elucidate potential functional properties of genes, and potentially to classify viruses.

Structure, function and therapeutic implications of OB-fold proteins: A lesson from past to present

Oligonucleotide/oligosaccharide-binding (OB)-fold proteins play essential roles in the regulation of genome and its correct transformation to the subsequent generation. To maintain the genomic stability, OB-fold proteins are implicated in various cellular processes including DNA replication, DNA repair, cell cycle regulation and maintenance of telomere. The diverse functional spectrums of OB-fold proteins are mainly due to their involvement in protein-DNA and protein-protein complexes. Mutations and consequential structural alteration in the OB-fold proteins often lead to severe diseases. Here, we have investigated the structure, function and mode of action of OB-fold proteins (RPA, BRCA2, DNA ligases and SSBs1/2) in cellular pathways and their relationship with diseases and their possible use in therapeutic intervention. Due to the crucial role of OB-fold proteins in regulating the key physiological process, a detailed structural understanding in the context of underlying mechanism of action and cellular complexity offers a new avenue to target OB-proteins for therapeutic intervention.

How RNA-Binding Proteins Interact with RNA: Molecules and Mechanisms

RNA-binding proteins (RBPs) comprise a large class of over 2,000 proteins that interact with transcripts in all manner of RNA-driven processes. The structures and mechanisms that RBPs use to bind and regulate RNA are incredibly diverse. In this review, we take a look at the components of protein-RNA interaction, from the molecular level to multi-component interaction. We first summarize what is known about protein-RNA molecular interactions based on analyses of solved structures. We additionally describe software currently available for predicting protein-RNA interaction and other resources useful for the study of RBPs. We then review the structure and function of seventeen known RNA-binding domains and analyze the hydrogen bonds adopted by protein-RNA structures on a domain-by-domain basis. We conclude with a summary of the higher-level mechanisms that regulate protein-RNA interactions.

Structural Features of Nucleoprotein CST/Shelterin Complex Involved in the Telomere Maintenance and Its Association with Disease Mutations

Telomere comprises the ends of eukaryotic linear chromosomes and is composed of G-rich (TTAGGG) tandem repeats which play an important role in maintaining genome stability, premature aging and onsets of many diseases. Majority of the telomere are replicated by conventional DNA replication, and only the last bit of the lagging strand is synthesized by telomerase (a reverse transcriptase). In addition to replication, telomere maintenance is principally carried out by two key complexes known as shelterin (TRF1, TRF2, TIN2, RAP1, POT1, and TPP1) and CST (CDC13/CTC1, STN1, and TEN1). Shelterin protects the telomere from DNA damage response (DDR) and regulates telomere length by telomerase; while, CST govern the extension of telomere by telomerase and C strand fill-in synthesis. We have investigated both structural and biochemical features of shelterin and CST complexes to get a clear understanding of their importance in the telomere maintenance. Further, we have analyzed ~115 clinically important mutations in both of the complexes. Association of such mutations with specific cellular fault unveils the importance of shelterin and CST complexes in the maintenance of genome stability. A possibility of targeting shelterin and CST by small molecule inhibitors is further investigated towards the therapeutic management of associated diseases. Overall, this review provides a possible direction to understand the mechanisms of telomere borne diseases, and their therapeutic intervention.

One evolutionarily selected amino acid variation is sufficient to provide functional specificity in the cold shock protein paralogs of Staphylococcus aureus

Bacterial genomes encode several families of protein paralogs. Discrimination between functional divergence and redundancy among paralogs is challenging due to their sequence conservation. Here, we investigated whether the amino acid differences present in the cold shock protein (CSP) paralogs of Staphylococcus aureus were responsible for functional specificity. Since deletion of cspA reduces the synthesis of staphyloxanthin (STX), we used it as an in vivo reporter of CSP functionality. Complementation of a ΔcspA strain with the different S. aureus CSP variants showed that only CspA could specifically restore STX production by controlling the activity of the stress‐associated sigma B factor (σ^B). To determine the amino acid residues responsible for CspA specificity, we created several chimeric CSPs that interchanged the amino acid differences between CspA and CspC, which shared the highest identity. We demonstrated that CspA Pro58 was responsible for the specific control of σ^B activity and its associated phenotypes. Interestingly, CspC gained the biological function of CspA when the E58P substitution was introduced. This study highlights how just one evolutionarily selected amino acid change may be sufficient to modify the specific functionality of CSP paralogs.