Vikram Alva
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View article: DNA Wrapping by a tetrameric bacterial histone
DNA Wrapping by a tetrameric bacterial histone Open
Histones are conserved DNA-packaging proteins found across all domains of life. In eukaryotes, canonical histones form octamers that wrap ~147 base pairs (bp) of DNA into nucleosomes, while in archaea they form dimers that polymerize into …
View article: ComFB, a widespread family of c-di-NMP receptor proteins
ComFB, a widespread family of c-di-NMP receptor proteins Open
Cyclic dimeric-GMP (c-di-GMP) is a ubiquitous bacterial second messenger that regulates a variety of cellular processes, including motility, biofilm formation, secretion, cell cycle progression, and development, and also contributes to the…
View article: Latent endogenous viral elements drive active infection and inheritance in a multicellular host
Latent endogenous viral elements drive active infection and inheritance in a multicellular host Open
Endogenous viral elements (EVEs) inserted in host genomes are often regarded as inert relics of past infections. Whether they can retain infective potential and contribute to active viral cycles has remained unresolved. Here, we demonstrat…
View article: Histone-mediated chromatin organization in prokaryotes and viruses
Histone-mediated chromatin organization in prokaryotes and viruses Open
Histones are fundamental chromatin-organizing proteins in eukaryotes and archaea, where they assemble into (hyper)nucleosomes that wrap DNA. Recent studies have expanded the known repertoire of histones, identifying new variants in both pr…
View article: DNA Wrapping by a Tetrameric Bacterial Histone
DNA Wrapping by a Tetrameric Bacterial Histone Open
Histones are conserved DNA-packaging proteins found across all domains of life. In eukaryotes, canonical histones form octamers that wrap ∼147 base pairs of DNA into nucleosomes — the fundamental units of chromatin. In archaea, histones fo…
View article: Mapping the ultrastructural topology of the corynebacterial cell surface
Mapping the ultrastructural topology of the corynebacterial cell surface Open
Corynebacterium glutamicum is a diderm bacterium extensively used in the industrial-scale production of amino acids. Corynebacteria belong to the bacterial family Mycobacteriaceae , which is characterized by a highly unusual cell envelope …
View article: Tissue-like multicellular development triggered by mechanical compression in archaea
Tissue-like multicellular development triggered by mechanical compression in archaea Open
The advent of clonal multicellularity is a critical evolutionary milestone, seen often in eukaryotes, rarely in bacteria, and only once in archaea. We show that uniaxial compression induces clonal multicellularity in haloarchaea, forming t…
View article: Donor Strand Complementation and Calcium Ion Coordination Drive the Chaperone-free Polymerization of Archaeal Cannulae
Donor Strand Complementation and Calcium Ion Coordination Drive the Chaperone-free Polymerization of Archaeal Cannulae Open
Cannulae are tubular protein filaments that accumulate on the extracellular surface of the hyperthermophilic archaeon Pyrodictium abyssi during cell division. Cannulae have been postulated to act as a primitive extracellular matrix through…
View article: ComFB, a new widespread family of c-di-NMP receptor proteins
ComFB, a new widespread family of c-di-NMP receptor proteins Open
Cyclic dimeric GMP (c-di-GMP) is a widespread bacterial second messenger that controls a variety of cellular functions, including protein and polysaccharide secretion, motility, cell division, cell development, and biofilm formation, and c…
View article: Tissue-Like Multicellular Development Triggered by Mechanical Compression in Archaea
Tissue-Like Multicellular Development Triggered by Mechanical Compression in Archaea Open
The advent of clonal multicellularity is a critical evolutionary milestone, seen often in eukaryotes, rarely in bacteria, and only once observed in archaea. We show that uniaxial compression induces clonal multicellularity in haloarchaea, …
View article: Halofilins as emerging bactofilin families of archaeal cell shape plasticity orchestrators
Halofilins as emerging bactofilin families of archaeal cell shape plasticity orchestrators Open
Bactofilins are rigid, nonpolar bacterial cytoskeletal filaments that link cellular processes to specific curvatures of the cytoplasmic membrane. Although homologs of bactofilins have been identified in archaea and eukaryotes, functional s…
View article: Histones and histone variant families in prokaryotes
Histones and histone variant families in prokaryotes Open
Histones are important chromatin-organizing proteins in eukaryotes and archaea. They form superhelical structures around which DNA is wrapped. Recent studies have shown that some archaea and bacteria contain alternative histones that exhib…
View article: Mapping the ultrastructural topology of the corynebacterial cell surface
Mapping the ultrastructural topology of the corynebacterial cell surface Open
Corynebacterium glutamicum is a diderm bacterium extensively used in the industrial-scale production of amino acids. Corynebacteria belong to the bacterial family Mycobacteriaceae , which is characterized by a highly unusual cell envelope …
View article: Bacterial histone HBb from <i>Bdellovibrio bacteriovorus</i> compacts DNA by bending
Bacterial histone HBb from <i>Bdellovibrio bacteriovorus</i> compacts DNA by bending Open
Histones are essential for genome compaction and transcription regulation in eukaryotes, where they assemble into octamers to form the nucleosome core. In contrast, archaeal histones assemble into dimers that form hypernucleosomes upon DNA…
View article: Membraneless channels sieve cations in ammonia-oxidizing marine archaea
Membraneless channels sieve cations in ammonia-oxidizing marine archaea Open
Nitrosopumilus maritimus is an ammonia-oxidizing archaeon that is crucial to the global nitrogen cycle 1,2 . A critical step for nitrogen oxidation is the entrapment of ammonium ions from a dilute marine environment at the cell surface and…
View article: Punctuated and continuous structural diversity of S-layers across the prokaryotic tree of life
Punctuated and continuous structural diversity of S-layers across the prokaryotic tree of life Open
Surface layers (S-layers) are two-dimensional (2D) crystalline lattices that frequently coat prokaryotic cells, playing a crucial role in protection, maintaining cellular integrity, and mediating environmental interactions. However, the mo…
View article: PII-like signaling proteins: a new paradigm in orchestrating cellular homeostasis
PII-like signaling proteins: a new paradigm in orchestrating cellular homeostasis Open
Members of the PII superfamily are versatile, multitasking signaling proteins ubiquitously found in all domains of life. They adeptly monitor and synchronize the cell's carbon, nitrogen, energy, redox, and diurnal states, primarily by bind…
View article: Halofilins as Emerging Bactofilin Families of Archaeal Cell Shape Plasticity Orchestrators
Halofilins as Emerging Bactofilin Families of Archaeal Cell Shape Plasticity Orchestrators Open
Bactofilins are rigid, non-polar bacterial cytoskeletal filaments that link cellular processes to specific curvatures of the cytoplasmic membrane. Although homologs of bactofilins have been identified in archaea and eukaryotes, functional …
View article: The cell envelope architecture of Deinococcus: HPI forms the S-layer and SlpA tethers the outer membrane to peptidoglycan
The cell envelope architecture of Deinococcus: HPI forms the S-layer and SlpA tethers the outer membrane to peptidoglycan Open
We compile 10 y of data from fieldwork in Samoa, a high fertility non-Western population, relevant to both evolutionary and biodevelopmental hypotheses for male androphilia (sexual attraction to adult males). One hypothesis is that mothers…
View article: pLM-BLAST: distant homology detection based on direct comparison of sequence representations from protein language models
pLM-BLAST: distant homology detection based on direct comparison of sequence representations from protein language models Open
Motivation The detection of homology through sequence comparison is a typical first step in the study of protein function and evolution. In this work, we explore the applicability of protein language models to this task. Results We introdu…
View article: Novel histones and histone variant families in prokaryotes
Novel histones and histone variant families in prokaryotes Open
Histones are important chromatin-organizing proteins in eukaryotes and archaea. They form superhelical structures around which DNA is wrapped. Recent studies have shown that some archaea and bacteria contain alternative histones that exhib…
View article: Architecture of the biofilm-associated archaic Chaperone-Usher pilus CupE from Pseudomonas aeruginosa
Architecture of the biofilm-associated archaic Chaperone-Usher pilus CupE from Pseudomonas aeruginosa Open
Chaperone-Usher Pathway (CUP) pili are major adhesins in Gram-negative bacteria, mediating bacterial adherence to biotic and abiotic surfaces. While classical CUP pili have been extensively characterized, little is known about so-called ar…
View article: Interdigitated immunoglobulin arrays form the hyperstable surface layer of the extremophilic bacterium <i>Deinococcus radiodurans</i>
Interdigitated immunoglobulin arrays form the hyperstable surface layer of the extremophilic bacterium <i>Deinococcus radiodurans</i> Open
Deinococcus radiodurans is an atypical diderm bacterium with a remarkable ability to tolerate various environmental stresses, due in part to its complex cell envelope encapsulated within a hyperstable surface layer (S-layer). Despite decad…
View article: Bacterial histone HBb from<i>Bdellovibrio bacteriovorus</i>compacts DNA by bending
Bacterial histone HBb from<i>Bdellovibrio bacteriovorus</i>compacts DNA by bending Open
Histones are essential for genome compaction and transcription regulation in eukaryotes, where they assemble into octamers to form the nucleosome core. In contrast, archaeal histones assemble into dimers that form hypernucleosomes upon DNA…
View article: pLM-BLAST – distant homology detection based on direct comparison of sequence representations from protein language models
pLM-BLAST – distant homology detection based on direct comparison of sequence representations from protein language models Open
Motivation The detection of homology through sequence comparison is a typical first step in the study of protein function and evolution. In this work, we explore the applicability of protein language models to this task. Results We introdu…
View article: Interdigitated immunoglobulin arrays form the hyperstable surface layer of the extremophilic bacterium <i>Deinococcus radiodurans</i>
Interdigitated immunoglobulin arrays form the hyperstable surface layer of the extremophilic bacterium <i>Deinococcus radiodurans</i> Open
Deinococcus radiodurans is an atypical diderm bacterium with a remarkable ability to tolerate various environmental stresses, partly because of its complex cell envelope encapsulated within a hyperstable surface layer (S-layer). Despite de…
View article: A multidomain connector links the outer membrane and cell wall in phylogenetically deep-branching bacteria
A multidomain connector links the outer membrane and cell wall in phylogenetically deep-branching bacteria Open
Deinococcus radiodurans is a phylogenetically deep-branching extremophilic bacterium that is remarkably tolerant to numerous environmental stresses, including large doses of ultraviolet (UV) radiation and extreme temperatures. It can even …
View article: A multi-domain connector links the outer membrane and cell wall in deep-branching bacteria
A multi-domain connector links the outer membrane and cell wall in deep-branching bacteria Open
Deinococcus radiodurans is a deep-branching extremophilic bacterium that is remarkably tolerant to numerous environmental stresses, including large doses of ultraviolet radiation and extreme temperatures. It can even survive in outer space…
View article: Architecture of the biofilm-associated archaic CupE pilus from<i>Pseudomonas aeruginosa</i>
Architecture of the biofilm-associated archaic CupE pilus from<i>Pseudomonas aeruginosa</i> Open
Chaperone-Usher Pathway (CUP) pili are major adhesins in Gram-negative bacteria, mediating bacterial adherence to biotic and abiotic surfaces. While classical CUP pili have been extensively characterized, little is known about so-called ar…