Comparison of methods for searching protein sequence databases.

We have compared commonly used sequence comparison algorithms, scoring matrices, and gap penalties using a method that identifies statistically significant differences in performance. Search sensitivity with either the Smith-Waterman algorithm or FASTA is significantly improved by using modern scoring matrices, such as BLOSUM45-55, and optimized gap penalties instead of the conventional PAM250 matrix. More dramatic improvement can be obtained by scaling similarity scores by the logarithm of the length of the library sequence (In()-scaling). With the best modern scoring matrix (BLOSUM55 or JO93) and optimal gap penalties (-12 for the first residue in the gap and -2 for additional residues), Smith-Waterman and FASTA performed significantly better than BLASTP. With In()-scaling and optimal scoring matrices (BLOSUM45 or Gonnet92) and gap penalties (-12, -1), the rigorous Smith-Waterman algorithm performs better than either BLASTP and FASTA, although with the Gonnet92 matrix the difference with FASTA was not significant. Ln()-scaling performed better than normalization based on other simple functions of library sequence length. Ln()-scaling also performed better than scores based on normalized variance, but the differences were not statistically significant for the BLOSUM50 and Gonnet92 matrices. Optimal scoring matrices and gap penalties are reported for Smith-Waterman and FASTA, using conventional or In()-scaled similarity scores. Searches with no penalty for gap extension, or no penalty for gap opening, or an infinite penalty for gaps performed significantly worse than the best methods. Differences in performance between FASTA and Smith-Waterman were not significant when partial query sequences were used. However, the best performance with complete query sequences was obtained with the Smith-Waterman algorithm and In()-scaling.     

Chlorophyll fluorescence in the leaves of Tradescantia species of different ecological groups: Induction events at different intensities of actinic light

Chlorophyll fluorescence analysis is one of the most convenient and widespread techniques used to monitor photosynthesis performance in plants. In this work, after a brief overview of the mechanisms of regulation of photosynthetic electron transport and protection of photosynthetic apparatus against photodamage, we describe results of our study of the effects of actinic light intensity on photosynthetic performance in Tradescantia species of different ecological groups. Using the chlorophyll fluorescence as a probe of photosynthetic activity, we have found that the shade-tolerant species Tradescantia fluminensis shows a higher sensitivity to short-term illumination (≤20 min) with low and moderate light (≤200 μE m⁻² s⁻¹) as compared with the light-resistant species Tradescantia sillamontana. In T. fluminensis, non-photochemical quenching of chlorophyll fluorescence (NPQ) and photosystem II operational efficiency (parameter Φ_PSII) saturate as soon as actinic light reaches ≈200 μE m⁻² s⁻¹. Otherwise, T. sillamontana revealed a higher capacity for NPQ at strong light (≥800 μE m⁻² s⁻¹). The post-illumination adaptation of shade-tolerant plants occurs slower than in the light-resistant species. The data obtained are discussed in terms of reactivity of photosynthetic apparatus to short-term variations of the environment light.     

The extracellular products of Anabaena cylindrica Lemm. I. Isolation of a macromolecular pigment-peptide complex and other components

The extracellular products of Anabaena cylindrica Lemm. comprise a large variety of compounds including peptides, brownish pigments and substances fluorescing white and blue in ultraviolet light. A number were separated or isolated using techniques of gel filtration, ion exchange and paper chromatography. Serine and threonine comprised over 90% of the amino acids in a group of complex pigmented and fluorescent compounds. One of these accounted for a large proportion of the peptide and pigment present. It contained a large pigment moiety of molecular weight > 5 000 which formed a firm complex with more than 10% of the iron supplied in the culture medium. The anti-polymyxin activity described by Whitton was not associated with any of the major pigments or peptides present.     

Consideration of the order Cryptonemiales and the families Nemastomataceae and Furcellariaceae (Gigartinales,Rhodophyta) in light of the morphology of Adelophyton corneum (J. Agardh) gen. et comb. nov. from southern Australia

A new red algal genus is described, based on the southern Australian Chaetangium corneum J. Agardh. It is reproductively unique in that while the auxiliary cell is intercalary in an adventitious filament, a defining character of the order Cryptonemiales, the vegetative structure, carpogonial branches, connecting filaments and gonimoblast development seem strongly allied to lower families of the Gigartinales. Although its predominantly thallus-inward gonimoblast development is characteristic of the gigartinalian family Furcellariaceae, it is suggested that the new alga should be placed in the Nemastomataceae and that this family exhibits features which, in an ancient algal stock, could theoretically have given rise to the lower cryptonemialian and higher gigartinalian lines. The possible relationships between the Nemastomataceae, Furcellariaceae and Solieriaceae are discussed, and some seemingly primitive features of the Nemastomataceae are enumcrated.     

SAR inspired by aldehyde oxidase (AO) metabolism: Discovery of novel,CNS penetrant tricyclic M4 PAMs

This letter describes progress towards an M₄ PAM preclinical candidate inspired by an unexpected aldehyde oxidase (AO) metabolite of a novel, CNS penetrant thieno[2,3-c]pyridine core to an equipotent, non-CNS penetrant thieno[2,3-c]pyrdin-7(6H)-one core. Medicinal chemistry design efforts yielded two novel tricyclic cores that enhanced M₄ PAM potency, regained CNS penetration, displayed favorable DMPK properties and afforded robust in vivo efficacy in reversing amphetamine-induced hyperlocomotion in rats.     

Pushing, pulling and trapping--modes of motor protein supported protein translocation

Protein translocation across the cellular membranes is an ubiquitous and crucial activity of cells. This process is mediated by translocases that consist of a protein conducting channel and an associated motor protein. Motor proteins interact with protein substrates and utilize the free energy of ATP binding and hydrolysis for protein unfolding, translocation and unbinding. Since motor proteins are found either at the cis- or trans-side of the membrane, different mechanisms for translocation have been proposed. In the Power stroke model, cis-acting motors are thought to push, while trans-motors pull on the substrate protein during translocation. In the Brownian ratchet model, translocation occurs by diffusion of the unfolded polypeptide through the translocation pore while directionality is achieved by trapping and refolding. Recent insights in the structure and function of the molecular motors suggest that different mechanisms can be employed simultaneously.     

Front Cover Image,Volume 116, Number 11, November 2019

CRISPR/Cas9-guided cytidine deaminase enables C:G to T:A base editing in bacterial genome without introduction of lethal double-stranded DNA break, supplement of foreign DNA template, or dependence on inefficient homologous recombination. However, limited by genome-targeting scope, editing window, and base transition capability, the application of base editing in metabolic engineering has not been explored. Herein, four Cas9 variants accepting different protospacer adjacent motif (PAM) sequences were used to increase the genome-targeting scope of bacterial base editing. After a comprehensive evaluation, we demonstrated that PAM requirement of bacterial base editing can be relaxed from NGG to NG using the Cas9 variants, providing 3.9-fold more target loci for gene inactivation in Corynebacterium glutamicum. Truncated or extended guide RNAs were employed to expand the canonical 5-bp editing window to 7-bp. Bacterial adenine base editing was also achieved with Cas9 fused to adenosine deaminase. With these updates, base editing can serve as an enabling tool for fast metabolic engineering. To demonstrate its potential, base editing was used to deregulate feedback inhibition of aspartokinase via amino acid substitution for lysine overproduction. Finally, a user-friendly online tool named gBIG was provided for designing guide RNAs for base editing-mediated inactivation of given genes in any given sequenced genome ( www.ibiodesign.net/gBIG ).     

大鼠甘氨肽酰化单氧酶在CHO细胞中的活性表达及在体外酰胺化修饰中的应用

将大鼠脑cDNA库来源的PAM基因片段,经克隆重组,构建成真核表达质粒pSV—PAM,并转染CH0细胞,获得在cHO中稳定表达活性型口α-酰胺化酶的细胞株DGAE。表达产物为双功能酶,分泌至培养基中的酶活力远高于胞内。体外酰胺化加工研究表明,以α—N—acetyl－Tyr-Val-Gly为底物,该酶催化反应的Km为12．Sμmol／L,V_max为180μmol／mg／h,而且催化反应中表现有最适铜离子浓度和pH值范围。表达的双功能酶可直接用于合成的多肽和基因工程表达产物的酰胺化加工修饰。