On the role, ecology, phylogeny, and structure of dual-family immunophilins

Protein-Ligand Interactions in Scarcity: The Stringent Response from Bacteria to Metazoa, and the Unanswered Questions

The stringent response, originally identified in Escherichia coli as a signal that leads to reprogramming of gene expression under starvation or nutrient deprivation, is now recognized as ubiquitous in all bacteria, and also as part of a broader survival strategy in diverse, other stress conditions. Much of our insight into this phenomenon derives from the role of hyperphosphorylated guanosine derivatives (pppGpp, ppGpp, pGpp; guanosine penta-, tetra- and tri-phosphate, respectively) that are synthesized on starvation cues and act as messengers or alarmones. These molecules, collectively referred to here as (p)ppGpp, orchestrate a complex network of biochemical steps that eventually lead to the repression of stable RNA synthesis, growth, and cell division, while promoting amino acid biosynthesis, survival, persistence, and virulence. In this analytical review, we summarize the mechanism of the major signaling pathways in the stringent response, consisting of the synthesis of the (p)ppGpp, their interaction with RNA polymerase, and diverse factors of macromolecular biosynthesis, leading to differential inhibition and activation of specific promoters. We also briefly touch upon the recently reported stringent-like response in a few eukaryotes, which is a very disparate mechanism involving MESH1 (Metazoan SpoT Homolog 1), a cytosolic NADPH phosphatase. Lastly, using ppGpp as an example, we speculate on possible pathways of simultaneous evolution of alarmones and their multiple targets.

Penetrating Exploration of Prognostic Correlations of the FKBP Gene Family with Lung Adenocarcinoma

The complexity of lung adenocarcinoma (LUAD), the development of which involves many interacting biological processes, makes it difficult to find therapeutic biomarkers for treatment. FK506-binding proteins (FKBPs) are composed of 12 members classified as conservative intracellular immunophilin family proteins, which are often connected to cyclophilin structures by tetratricopeptide repeat domains and have peptidyl prolyl isomerase activity that catalyzes proline from residues and turns the trans form into the cis form. Since FKBPs belong to chaperone molecules and promote protein folding, previous studies demonstrated that FKBP family members significantly contribute to the degradation of damaged, misfolded, abnormal, and foreign proteins. However, transcript expressions of this gene family in LUAD still need to be more fully investigated. In this research, we adopted high-throughput bioinformatics technology to analyze FKBP family genes in LUAD to provide credible information to clinicians and promote the development of novel cancer target drugs in the future. The current data revealed that the messenger (m)RNA levels of FKBP2, FKBP3, FKBP4, FKBP10, FKBP11, and FKBP14 were overexpressed in LUAD, and FKBP10 had connections to poor prognoses among LUAD patients in an overall survival (OS) analysis. Based on the above results, we selected FKBP10 to further conduct a comprehensive analysis of the downstream pathway and network. Through a DAVID analysis, we found that FKBP10 was involved in mitochondrial electron transport, NADH to ubiquinone transport, mitochondrial respiratory chain complex I assembly, etc. The MetaCore pathway analysis also indicated that FKBP10 was involved in "Ubiquinone metabolism", "Translation_(L)-selenoaminoacid incorporation in proteins during translation", and "Transcription_Negative regulation of HIF1A function". Collectively, this study revealed that FKBP family members are both significant prognostic biomarkers for lung cancer progression and promising clinical therapeutic targets, thus providing new targets for treating LUAD patients.

Evolution of Protein Structure and Stability in Global Warming

This review focuses on the molecular signatures of protein structures in relation to evolution and survival in global warming. It is based on the premise that the power of evolutionary selection may lead to thermotolerant organisms that will repopulate the planet and continue life in general, but perhaps with different kinds of flora and fauna. Our focus is on molecular mechanisms, whereby known examples of thermoresistance and their physicochemical characteristics were noted. A comparison of interactions of diverse residues in proteins from thermophilic and mesophilic organisms, as well as reverse genetic studies, revealed a set of imprecise molecular signatures that pointed to major roles of hydrophobicity, solvent accessibility, disulfide bonds, hydrogen bonds, ionic and π-electron interactions, and an overall condensed packing of the higher-order structure, especially in the hydrophobic regions. Regardless of mutations, specialized protein chaperones may play a cardinal role. In evolutionary terms, thermoresistance to global warming will likely occur in stepwise mutational changes, conforming to the molecular signatures, such that each "intermediate" fits a temporary niche through punctuated equilibrium, while maintaining protein functionality. Finally, the population response of different species to global warming may vary substantially, and, as such, some may evolve while others will undergo catastrophic mass extinction.

Protein Tetratricopeptide Repeat and the Companion Non-tetratricopeptide Repeat Helices: Bioinformatic Analysis of Interhelical Interactions

The tetratricopeptide repeat (TPR) of proteins consists of a 34-amino acid, alpha-helical motif that comprises a pattern of small and large hydrophobic residues, leading to a recognizable signature sequence. Structural and functional studies have documented that tandem TPRs form a superhelix that interacts with client molecules through strategically placed amino acids. Interestingly, most of the known TPRs are flanked by alpha-helices that lack the TPR signature but often appear as a continuation of the TPR superhelix. The exact role and specificity of these TPR-accompanying non-TPR helices have remained a mystery. Here, starting with TPR proteins of known structure, bioinformatic analyses were conducted on these helices, which revealed that they are diverse in sequence, lacking a clear consensus. However, they display significant atomic contacts with the nearest TPR helix and, to some extent, with the next TPR helix over. The majority of these contacts do not use the signature residues of the TPR helix but rather involve hydrophobic side chains on the facing sides. Thus, compared with the TPR helices, these companion helices are generic in nature, and seem to serve as relatively passive gatekeepers, leaving the terminal TPR helices to encode the signature residues that interact with cognate clients.

Dual-Family Peptidylprolyl Isomerases (Immunophilins) of Select Monocellular Organisms

The dual-family peptidylprolyl cis-trans isomerases (immunophilins) represent a naturally occurring chimera of the classical FK506-binding protein (FKBP) and cyclophilin (CYN), connected by a flexible linker. They are found exclusively in monocellular organisms. The modular builds of these molecules represent two distinct types: CYN-(linker)-FKBP and FKBP-3TPR (tetratricopeptide repeat)-CYN. Abbreviated respectively as CFBP and FCBP, the two classes also exhibit distinct organism preference, the CFBP being found in prokaryotes, and the FCBP in eukaryotes. This review summarizes the mystery of these unique class of prolyl isomerases, focusing on their host organisms, potential physiological role, and likely routes of evolution.

A Family of Novel Cyclophilins, Conserved in the Mimivirus Genus of the Giant DNA Viruses

The cyclophilin (abbreviated here as CYN) family represents a large group of protein prolyl isomerase (PPIase), many of which are also chaperones that promote proper folding of a large variety of client proteins. Over the past few years, megaviruses with giant DNA genomes were discovered and placed in the order Megavirales. Recently, the first complete genome sequence of Acanthamoebaae polyphaga mimivirus, a member of the Mimiviridae family of the Megavirales order, revealed a novel CYN that lacked PPIase activity and contained unique peptide insertions. To examine the universality of this unique CYN, I have reviewed and compared all CYN sequences found in the Megavirales genomes that are currently available. The results showed that multiple unique sequence features are indeed highly conserved in CYNs of all members of the Mimivirus genus, whereas viruses of the other genera of this family encode canonical CYNs only. Overall, the primary structures of all Mimivirus CYNs were highly similar, but different from those in the other genera, although the higher order structures were conserved across genera. In summary, this review establishes a family of novel but conserved cyclophilins that occur in a single viral genus.

Bioinformatic Analysis Reveals Conservation of Intrinsic Disorder in the Linker Sequences of Prokaryotic Dual-family Immunophilin Chaperones

The two classical immunophilin families, found essentially in all living cells, are: cyclophilin (CYN) and FK506-binding protein (FKBP). We previously reported a novel class of immunophilins that are natural chimera of these two, which we named dual-family immunophilin (DFI). The DFIs were found in either of two conformations: CYN-linker-FKBP (CFBP) or FKBP-3TPR-CYN (FCBP). While the 3TPR domain can serve as a flexible linker between the FKBP and CYN modules in the FCBP-type DFI, the linker sequences in the CFBP-type DFIs are relatively short, diverse in sequence, and contain no discernible motif or signature. Here, I present several lines of computational evidence that, regardless of their primary structure, these CFBP linkers are intrinsically disordered. This report provides the first molecular foundation for the model that the CFBP linker acts as an unstructured, flexible loop, allowing the two flanking chaperone modules function independently while linked in cis, likely to assist in the folding of multisubunit client complexes.

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Dual-family immunophilins (DFIs) are recently discovered chimeric chaperones.

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Bacterial DFIs possess the structure CYN-linker-FKBP, abbreviated as CFBP.

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The linker sequences in CFBP are diverse but possess intrinsic disorder (ID).

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The large CFBP linker with ID is a novel discovery in prokaryotes.

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ID befits the linker's role as a flexible connector between two chaperone modules.

Microbial cyclophilins: specialized functions in virulence and beyond

Cyclophilins belong to the superfamily of peptidyl-prolyl cis/trans isomerases (PPIases, EC: 5.2.1.8), the enzymes that catalyze the cis/trans isomerization of peptidyl-prolyl peptide bonds in unfolded and partially folded polypeptide chains and native state proteins. Cyclophilins have been extensively studied, since they are involved in multiple cellular processes related to human pathologies, such as neurodegenerative disorders, infectious diseases, and cancer. However, the presence of cyclophilins in all domains of life indicates a broader biological importance. In this mini-review, we summarize current advances in the study of microbial cyclophilins. Apart from their anticipated role in protein folding and chaperoning, cyclophilins are involved in several other biological processes, such as cellular signal transduction, adaptation to stress, control of pathogens virulence, and modulation of host immune response. Since many existing family members do not have well-defined functions and novel ones are being characterized, the requirement for further studies on their biological role and molecular mechanism of action is apparent.