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Article ; Online: De Novo

Nishikawa, Shota / Watanabe, Hidenori / Terasaka, Naohiro / Katoh, Takayuki / Fujishima, Kosuke

Biomacromolecules

2023 Volume 25, Issue 1, Page(s) 355–365

Abstract: RNA-binding proteins participate in diverse cellular processes, including DNA repair, post-transcriptional modification, and cancer progression through their interactions with RNAs, making them attractive for biotechnological applications. While nature ... ...

Abstract	RNA-binding proteins participate in diverse cellular processes, including DNA repair, post-transcriptional modification, and cancer progression through their interactions with RNAs, making them attractive for biotechnological applications. While nature provides an array of naturally occurring RNA-binding proteins, developing
MeSH term(s)	RNA, Messenger/chemistry ; Peptides/chemistry ; Codon ; RNA ; RNA-Binding Proteins/genetics
Chemical Substances	RNA, Messenger ; Peptides ; Codon ; RNA (63231-63-0) ; RNA-Binding Proteins
Language	English
Publishing date	2023-12-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1526-4602
ISSN (online)	1526-4602
DOI	10.1021/acs.biomac.3c01024
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Article ; Online: One-Pot

Wang, Po-Hsiang / Nishikawa, Shota / McGlynn, Shawn Erin / Fujishima, Kosuke

ACS synthetic biology

2023 Volume 12, Issue 10, Page(s) 2887–2896

Abstract: Fe-S clusters are essential cofactors mediating electron transfer in respiratory and metabolic networks. However, obtaining active [4Fe-4S] proteins with heterologous expression is challenging due to (i) the requirements for [4Fe-4S] cluster assembly, ( ... ...

Abstract	Fe-S clusters are essential cofactors mediating electron transfer in respiratory and metabolic networks. However, obtaining active [4Fe-4S] proteins with heterologous expression is challenging due to (i) the requirements for [4Fe-4S] cluster assembly, (ii) the O
MeSH term(s)	Iron-Sulfur Proteins/genetics ; Iron-Sulfur Proteins/metabolism ; Escherichia coli/metabolism ; NAD/metabolism ; Ferredoxins/genetics ; Ferredoxins/metabolism ; Aconitate Hydratase/metabolism ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism ; Oxidoreductases/genetics ; Oxidoreductases/metabolism ; Flavins/metabolism
Chemical Substances	Iron-Sulfur Proteins ; NAD (0U46U6E8UK) ; Ferredoxins ; Aconitate Hydratase (EC 4.2.1.3) ; Recombinant Proteins ; Oxidoreductases (EC 1.-) ; Flavins
Language	English
Publishing date	2023-07-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2161-5063
ISSN (online)	2161-5063
DOI	10.1021/acssynbio.3c00155
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Article ; Online: Sequencing the origins of life.

Jia, Tony Z / Nishikawa, Shota / Fujishima, Kosuke

BBA advances

2022 Volume 2, Page(s) 100049

Abstract: One goal of origins of life research is to understand how primitive informational and catalytic biopolymers emerged and evolved. Recently, a number of sequencing techniques have been applied to analysis of replicating and evolving primitive biopolymer ... ...

Abstract	One goal of origins of life research is to understand how primitive informational and catalytic biopolymers emerged and evolved. Recently, a number of sequencing techniques have been applied to analysis of replicating and evolving primitive biopolymer systems, providing a sequence-specific and high-resolution view of primitive chemical processes. Here, we review application of sequencing techniques to analysis of synthetic and primitive nucleic acids and polypeptides. This includes next-generation sequencing of primitive polymerization and evolution processes, followed by discussion of other novel biochemical techniques that could contribute to sequence analysis of primitive biopolymer driven chemical systems. Further application of sequencing to origins of life research, perhaps as a life detection technology, could provide insight into the origin and evolution of informational and catalytic biopolymers on early Earth or elsewhere.
Language	English
Publishing date	2022-03-05
Publishing country	Netherlands
Document type	Journal Article ; Review
ISSN	2667-1603
ISSN (online)	2667-1603
DOI	10.1016/j.bbadva.2022.100049
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Article: Sequencing the origins of life

Jia, Tony Z. / Nishikawa, Shota / Fujishima, Kosuke

BBA advances. 2022, v. 2

2022

Abstract	One goal of origins of life research is to understand how primitive informational and catalytic biopolymers emerged and evolved. Recently, a number of sequencing techniques have been applied to analysis of replicating and evolving primitive biopolymer systems, providing a sequence-specific and high-resolution view of primitive chemical processes. Here, we review application of sequencing techniques to analysis of synthetic and primitive nucleic acids and polypeptides. This includes next-generation sequencing of primitive polymerization and evolution processes, followed by discussion of other novel biochemical techniques that could contribute to sequence analysis of primitive biopolymer driven chemical systems. Further application of sequencing to origins of life research, perhaps as a life detection technology, could provide insight into the origin and evolution of informational and catalytic biopolymers on early Earth or elsewhere.
Keywords	biopolymers ; evolution ; polymerization ; polypeptides
Language	English
Publishing place	Elsevier B.V.
Document type	Article
ISSN	2667-1603
DOI	10.1016/j.bbadva.2022.100049
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Article ; Online: Peptides before and during the nucleotide world: an origins story emphasizing cooperation between proteins and nucleic acids.

Fried, Stephen D / Fujishima, Kosuke / Makarov, Mikhail / Cherepashuk, Ivan / Hlouchova, Klara

Journal of the Royal Society, Interface

2022 Volume 19, Issue 187, Page(s) 20210641

Abstract: Recent developments in Origins of Life research have focused on substantiating the narrative of an abiotic emergence of nucleic acids from organic molecules of low molecular weight, a paradigm that typically sidelines the roles of peptides. Nevertheless, ...

Abstract	Recent developments in Origins of Life research have focused on substantiating the narrative of an abiotic emergence of nucleic acids from organic molecules of low molecular weight, a paradigm that typically sidelines the roles of peptides. Nevertheless, the simple synthesis of amino acids, the facile nature of their activation and condensation, their ability to recognize metals and cofactors and their remarkable capacity to self-assemble make peptides (and their analogues) favourable candidates for one of the earliest functional polymers. In this mini-review, we explore the ramifications of this hypothesis. Diverse lines of research in molecular biology, bioinformatics, geochemistry, biophysics and astrobiology provide clues about the progression and early evolution of proteins, and lend credence to the idea that early peptides served many central prebiotic roles before they were encodable by a polynucleotide template, in a putative 'peptide-polynucleotide stage'. For example, early peptides and mini-proteins could have served as catalysts, compartments and structural hubs. In sum, we shed light on the role of early peptides and small proteins
MeSH term(s)	Nucleic Acids ; Nucleotides ; Origin of Life ; Peptides/chemistry ; Proteins
Chemical Substances	Nucleic Acids ; Nucleotides ; Peptides ; Proteins
Language	English
Publishing date	2022-02-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2156283-0
ISSN	1742-5662 ; 1742-5689
ISSN (online)	1742-5662
ISSN	1742-5689
DOI	10.1098/rsif.2021.0641
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Article ; Online: Modern and prebiotic amino acids support distinct structural profiles in proteins.

Tretyachenko, Vyacheslav / Vymětal, Jiří / Neuwirthová, Tereza / Vondrášek, Jiří / Fujishima, Kosuke / Hlouchová, Klára

Open biology

2022 Volume 12, Issue 6, Page(s) 220040

Abstract: The earliest proteins had to rely on amino acids available on early Earth before the biosynthetic pathways for more complex amino acids evolved. In extant proteins, a significant fraction of the 'late' amino acids (such as Arg, Lys, His, Cys, Trp and Tyr) ...

Abstract	The earliest proteins had to rely on amino acids available on early Earth before the biosynthetic pathways for more complex amino acids evolved. In extant proteins, a significant fraction of the 'late' amino acids (such as Arg, Lys, His, Cys, Trp and Tyr) belong to essential catalytic and structure-stabilizing residues. How (or if) early proteins could sustain an early biosphere has been a major puzzle. Here, we analysed two combinatorial protein libraries representing proxies of the available sequence space at two different evolutionary stages. The first is composed of the entire alphabet of 20 amino acids while the second one consists of only 10 residues (ASDGLIPTEV) representing a consensus view of plausibly available amino acids through prebiotic chemistry. We show that compact conformations resistant to proteolysis are surprisingly similarly abundant in both libraries. In addition, the early alphabet proteins are inherently more soluble and refoldable, independent of the general Hsp70 chaperone activity. By contrast, chaperones significantly increase the otherwise poor solubility of the modern alphabet proteins suggesting their coevolution with the amino acid repertoire. Our work indicates that while both early and modern amino acids are predisposed to supporting protein structure, they do so with different biophysical properties and via different mechanisms.
MeSH term(s)	Amino Acids/chemistry ; Prebiotics ; Protein Folding ; Proteins/chemistry
Chemical Substances	Amino Acids ; Prebiotics ; Proteins
Language	English
Publishing date	2022-06-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2630944-0
ISSN	2046-2441 ; 2046-2441
ISSN (online)	2046-2441
ISSN	2046-2441
DOI	10.1098/rsob.220040
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Article ; Online: CoLiDe: Combinatorial Library Design tool for probing protein sequence space.

Tretyachenko, Vyacheslav / Voráček, Václav / Souček, Radko / Fujishima, Kosuke / Hlouchová, Klára

Bioinformatics (Oxford, England)

2020 Volume 37, Issue 4, Page(s) 482–489

Abstract: Motivation: Current techniques of protein engineering focus mostly on re-designing small targeted regions or defined structural scaffolds rather than constructing combinatorial libraries of versatile compositions and lengths. This is a missed ... ...

Abstract	Motivation: Current techniques of protein engineering focus mostly on re-designing small targeted regions or defined structural scaffolds rather than constructing combinatorial libraries of versatile compositions and lengths. This is a missed opportunity because combinatorial libraries are emerging as a vital source of novel functional proteins and are of interest in diverse research areas. Results: Here, we present a computational tool for Combinatorial Library Design (CoLiDe) offering precise control over protein sequence composition, length and diversity. The algorithm uses evolutionary approach to provide solutions to combinatorial libraries of degenerate DNA templates. We demonstrate its performance and precision using four different input alphabet distribution on different sequence lengths. In addition, a model design and experimental pipeline for protein library expression and purification is presented, providing a proof-of-concept that our protocol can be used to prepare purified protein library samples of up to 1011-1012 unique sequences. CoLiDe presents a composition-centric approach to protein design towards different functional phenomena. Availabilityand implementation: CoLiDe is implemented in Python and freely available at https://github.com/voracva1/CoLiDe. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Algorithms ; Amino Acid Sequence ; Gene Library ; Protein Engineering ; Proteins/genetics ; Software
Chemical Substances	Proteins
Language	English
Publishing date	2020-09-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btaa804
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Article ; Online: In Vitro Evolution Reveals Noncationic Protein-RNA Interaction Mediated by Metal Ions.

Giacobelli, Valerio G / Fujishima, Kosuke / Lepšík, Martin / Tretyachenko, Vyacheslav / Kadavá, Tereza / Makarov, Mikhail / Bednárová, Lucie / Novák, Petr / Hlouchová, Klára

Molecular biology and evolution

2022 Volume 39, Issue 3

Abstract: RNA-peptide/protein interactions have been of utmost importance to life since its earliest forms, reaching even before the last universal common ancestor (LUCA). However, the ancient molecular mechanisms behind this key biological interaction remain ... ...

Abstract	RNA-peptide/protein interactions have been of utmost importance to life since its earliest forms, reaching even before the last universal common ancestor (LUCA). However, the ancient molecular mechanisms behind this key biological interaction remain enigmatic because extant RNA-protein interactions rely heavily on positively charged and aromatic amino acids that were absent (or heavily under-represented) in the early pre-LUCA evolutionary period. Here, an RNA-binding variant of the ribosomal uL11 C-terminal domain was selected from an approximately 1010 library of partially randomized sequences, all composed of ten prebiotically plausible canonical amino acids. The selected variant binds to the cognate RNA with a similar overall affinity although it is less structured in the unbound form than the wild-type protein domain. The variant complex association and dissociation are both slower than for the wild-type, implying different mechanistic processes involved. The profile of the wild-type and mutant complex stabilities along with molecular dynamics simulations uncovers qualitative differences in the interaction modes. In the absence of positively charged and aromatic residues, the mutant uL11 domain uses ion bridging (K+/Mg2+) interactions between the RNA sugar-phosphate backbone and glutamic acid residues as an alternative source of stabilization. This study presents experimental support to provide a new perspective on how early protein-RNA interactions evolved, where the lack of aromatic/basic residues may have been compensated by acidic residues plus metal ions.
MeSH term(s)	Amino Acids/genetics ; Ions ; Molecular Dynamics Simulation ; RNA/genetics
Chemical Substances	Amino Acids ; Ions ; RNA (63231-63-0)
Language	English
Publishing date	2022-02-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	998579-7
ISSN	1537-1719 ; 0737-4038
ISSN (online)	1537-1719
ISSN	0737-4038
DOI	10.1093/molbev/msac032
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Article: tRNA gene diversity in the three domains of life.

Fujishima, Kosuke / Kanai, Akio

Frontiers in genetics

2014 Volume 5, Page(s) 142

Abstract: Transfer RNA (tRNA) is widely known for its key role in decoding mRNA into protein. Despite their necessity and relatively short nucleotide sequences, a large diversity of gene structures and RNA secondary structures of pre-tRNAs and mature tRNAs have ... ...

Abstract	Transfer RNA (tRNA) is widely known for its key role in decoding mRNA into protein. Despite their necessity and relatively short nucleotide sequences, a large diversity of gene structures and RNA secondary structures of pre-tRNAs and mature tRNAs have recently been discovered in the three domains of life. Growing evidences of disrupted tRNA genes in the genomes of Archaea reveals unique gene structures such as, intron-containing tRNA, split tRNA, and permuted tRNA. Coding sequence for these tRNAs are either separated with introns, fragmented, or permuted at the genome level. Although evolutionary scenario behind the tRNA gene disruption is still unclear, diversity of tRNA structure seems to be co-evolved with their processing enzyme, so-called RNA splicing endonuclease. Metazoan mitochondrial tRNAs (mtRNAs) are known for their unique lack of either one or two arms from the typical tRNA cloverleaf structure, while still maintaining functionality. Recently identified nematode-specific V-arm containing tRNAs (nev-tRNAs) possess long variable arms that are specific to eukaryotic class II tRNA(Ser) and tRNA(Leu) but also decode class I tRNA codons. Moreover, many tRNA-like sequences have been found in the genomes of different organisms and viruses. Thus, this review is aimed to cover the latest knowledge on tRNA gene diversity and further recapitulate the evolutionary and biological aspects that caused such uniqueness.
Language	English
Publishing date	2014-05-26
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2014.00142
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Article ; Online: Aqueous breakdown of aspartate and glutamate to n-ω-amino acids on the parent bodies of carbonaceous chondrites and asteroid Ryugu.

Li, Yamei / Kurokawa, Hiroyuki / Sekine, Yasuhito / Kebukawa, Yoko / Nakano, Yuko / Kitadai, Norio / Zhang, Naizhong / Zang, Xiaofeng / Ueno, Yuichiro / Fujimori, Gen / Nakamura, Ryuhei / Fujishima, Kosuke / Isa, Junko

Science advances

2023 Volume 9, Issue 50, Page(s) eadh7845

Abstract: Amino acids in carbonaceous chondrites may have seeded the origin of life on Earth and possibly elsewhere. Recently, the return samples from a C-type asteroid Ryugu were found to contain amino acids with a similar distribution to Ivuna-type CI chondrites, ...

Abstract	Amino acids in carbonaceous chondrites may have seeded the origin of life on Earth and possibly elsewhere. Recently, the return samples from a C-type asteroid Ryugu were found to contain amino acids with a similar distribution to Ivuna-type CI chondrites, suggesting the potential of amino acid abundances as molecular descriptors of parent body geochemistry. However, the chemical mechanisms responsible for the amino acid distributions remain to be elucidated particularly at low temperatures (<50°C). Here, we report that two representative proteinogenic amino acids, aspartic acid and glutamic acid, decompose to β-alanine and γ-aminobutyric acid, respectively, under simulated geoelectrochemical conditions at 25°C. This low-temperature conversion provides a plausible explanation for the enrichment of these two n-ω-amino acids compared to their precursors in heavily aqueously altered CI chondrites and Ryugu's return samples. The results suggest that these heavily aqueously altered samples originated from the water-rich mantle of their water/rock differentiated parent planetesimals where protein α-amino acids were decomposed.
MeSH term(s)	Aspartic Acid ; Glutamic Acid ; Meteoroids ; Amino Acids/chemistry ; Water
Chemical Substances	Aspartic Acid (30KYC7MIAI) ; Glutamic Acid (3KX376GY7L) ; Amino Acids ; Water (059QF0KO0R)
Language	English
Publishing date	2023-12-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.adh7845
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